Methods and compositions for the molecular diagnosis of microsatellite instability and treatments for cancer

ABSTRACT

Described herein are methods and compositions related to treatments for cancer. Various embodiments relate to the determination of microsatellite instability as a marker for the likelihood of whether a given cancer will respond to certain therapies, including checkpoint inhibitor immunotherapies, and methods of treatment based upon those determinations.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 63/044,029 filed Jun. 25, 2020, the contents of which are incorporated herein by reference in their entirety.

GOVERNMENT SUPPORT

This invention was made with government support under Grant No. CA222344, awarded by the National Institutes of Health. The government has certain rights in the invention.

TECHNICAL FIELD

The technology described herein relates to methods of diagnosing and treating cancer.

BACKGROUND

Microsatellite instability (MSI) is a molecular tumor phenotype that is indicative of genomic hypermutability, usually reflecting inactivation of the mismatch repair (MMR) system. MSI is marked by spontaneous gains or losses of nucleotides from repetitive DNA tracts, resulting in new alleles of differing length that serve as the basis for its clinical diagnosis. Although classically associated with colorectal and endometrial tumors, MSI has now been recognized in most cancer types with varying prevalence and is accompanied by a generally increased rate of mutations genome-wide. Molecular diagnosis of MSI can be predictive of a patient's response to an anti-cancer therapy. However, there is an unmet need for cancer screening panels of MSI in specific cancer types and the microsatellite marker sequences vary between different types of cancers.

SUMMARY

To better inform molecular diagnosis of MSI, over 9,000 tumor-normal exome pairs and over 900 whole genome sequence pairs were examined from 33 different cancer types and cataloged for genome-wide microsatellite instability events. Using a statistical framework, microsatellite mutations that were predictive of MSI within and across cancer types were identified. The diagnostic accuracy of different subsets of maximally informative markers was estimated computationally using a dedicated validation set. Based on these analyses, twenty-five cancer types exhibited hypermutated states consistent with MSI. Recurrently mutated microsatellites associated with MSI were identifiable in 15 cancer types, but were largely specific to individual cancer types. Cancer-specific microsatellite panels of one to seven loci were needed to attain 95% diagnostic sensitivity and specificity for 11 cancer types, and in eight of the cancer types, 100% sensitivity and specificity were achieved. In contrast, breast cancer required 800 loci to achieve comparable performance, and it was not possible to identify recurrent microsatellite mutations supporting reliable MSI diagnosis in ovarian tumors. Thus, as described further herein below, most microsatellites informative for MSI are specific to particular cancer types, requiring the use of tissue-specific loci for optimal diagnosis. Accordingly, limited numbers of markers are needed to provide accurate MSI diagnosis in most tumor types, but it is challenging to diagnose breast and ovarian cancers using pre-defined microsatellite locus panels.

Features associated with informative microsatellites were cataloged, and sets of microsatellites are ranked herein according to degree of predictive value for each microsatellite for each tumor type and underpin diagnostic, prognostic and therapeutic methods as described herein below. For each set, the number of mutated members of that set which are determinative of MSI-H is influenced by where the mutated members of the set are in the rank ordering, with higher ranked microsatellite markers carrying greater weight (i.e., lower p-value). Thus, the number of microsatellite mutations necessary for a sensitive and specific determination of MSI-H for a given cancer type can vary depending upon the ranking of the mutated markers in the set, with fewer mutations needed to assign the cancer to the MSI-H category when the mutations detected are in higher ranked microsatellites (i.e., lower p-value).

Accordingly, in one aspect, described herein is a method of predicting whether a subject's cancer will respond to checkpoint inhibitor immunotherapy, the method comprising: (a) receiving microsatellite instability data for a defined set of microsatellite repeat marker sequences in cells of the subject's cancer; and (b) processing the microsatellite instability data to output a categorical measure of microsatellite instability high (MSI-H) or microsatellite stable (MSS); wherein when the subject's cancer is determined to exhibit MSI-H, it is predicted that the cancer will respond to checkpoint inhibitor immunotherapy, and when the subject's cancer is determined to exhibit MSS, it is predicted that the cancer is less likely to respond to checkpoint inhibitor immunotherapy.

In another aspect, described herein is a method of predicting whether a subject's cancer will respond to checkpoint inhibitor immunotherapy, the method comprising: determining microsatellite instability status for a defined set of microsatellite repeat marker sequences in cells of the subject's cancer, wherein determining the microsatellite instability status of the subject's cancer comprises: (i) assaying loci in the defined set of microsatellite repeat marker sequences in cells of the subject's cancer for mutation, thereby generating microsatellite instability data; and (ii) processing the microsatellite instability data to output a categorical measure of microsatellite instability high (MSI-H) status or microsatellite stable (MSS) status for the subject's cancer; wherein when the subject's cancer is determined to exhibit MSI-H, it is predicted that the cancer will respond to checkpoint inhibitor immunotherapy, and when the subject's cancer is determined to exhibit MSS, it is predicted that the cancer is less likely to respond to checkpoint inhibitor immunotherapy.

In another aspect, described herein is a method of determining microsatellite instability (MSI) in a subject's cancer, the method comprising: assaying mutation status for a set of microsatellite repeat marker sequences in cells of the subject's cancer, wherein when the set of microsatellites exhibits mutation at or above a threshold number of microsatellites in the set, the subject's cancer is determined to exhibit high microsatellite instability (MSI-H), and when the set of microsatellites exhibits mutation below the threshold number of microsatellites in the set, the subject's cancer is determined to exhibit microsatellite stability (MSS); wherein the threshold for the set is determined using the percentage of mutated microsatellite markers in the set to calculate the area under the receiver operating characteristic (AUROC), and wherein the smallest number of markers in the set necessary to reach an AUROC value selected in the range of 0.6 to 0.99, inclusive, is the threshold.

In another aspect, described herein is a method of treating cancer in a subject in need thereof, the method comprising determining microsatellite instability status for cells of a subject's cancer by a method of described herein, and, when the microsatellite instability status is determined to be MSI-H, administering a checkpoint inhibitor, or, when the microsatellite instability status is determined to be MSS, administering a non-checkpoint inhibitor cancer therapeutic.

In another aspect, described herein is a method of treating cancer in a subject in need thereof, wherein the subject's cancer has been determined to have a microsatellite instability status of MSI-H as determined by a method as described herein, the method comprising administering an effective amount of a checkpoint inhibitor to the subject.

In another aspect, described herein is a method of predicting whether a subject's cancer will respond to checkpoint inhibitor immunotherapy, the method comprising: assaying mutation status for a set of microsatellite repeat marker sequences in cells of the subject's cancer, wherein when mutations are present in at least a threshold number of markers in the set, the set provides at least 95% sensitivity and at least 95% specificity for predicting high microsatellite instability (MSI-H) for the subject's tumor.

In another aspect, described herein is a method of determining microsatellite instability (MSI) in a subject's cancer, the method comprising: assaying mutation status for a set of microsatellite repeat marker sequences in the cells of the subject's cancer, wherein when mutations are present in at least a threshold number of markers in the set, the set provides at least 95% sensitivity and at least 95% specificity for predicting high microsatellite instability (MSI-H) for the subject's tumor.

In another aspect, described herein is a method of treating cancer in a subject in need thereof, the method comprising: assaying mutation status for a set of microsatellite repeat marker sequences in cells of the subject's cancer, wherein when mutations are present in at least a threshold number of markers in the set, the set provides at least 95% sensitivity and at least 95% specificity for predicting high microsatellite instability (MSI-H) for the subject's tumor.

In another aspect, described herein is a use of a checkpoint inhibitor for the treatment of cancer, comprising: (a) receiving microsatellite instability data for a defined set of microsatellite repeat marker sequences in cells of the subject's cancer; and (b) processing the microsatellite instability data to output a categorical measure of microsatellite instability high (MSI-H) or microsatellite stable (MSS); wherein the checkpoint inhibitor is administered when the subject's cancer is determined to exhibit MSI-H.

In another aspect, described herein is a use of a checkpoint inhibitor for the treatment of cancer, comprising: determining microsatellite instability status for a defined set of microsatellite repeat marker sequences in cells of the subject's cancer, wherein determining the microsatellite instability status of the subject's cancer comprises: (i) assaying loci in the defined set of microsatellite repeat marker sequences in cells of the subject's cancer for mutation, thereby generating microsatellite instability data; and (ii) processing the microsatellite instability data to output a categorical measure of microsatellite instability high (MSI-H) status or microsatellite stable (MSS) status for the subject's cancer; wherein the checkpoint inhibitor is administered when the subject's cancer is determined to exhibit MSI-H.

In another aspect, described herein is a diagnostic kit for determining microsatellite instability in a cancer, the kit comprising reagents that permit the detection of microsatellite mutation in a set of microsatellite repeat marker sequences in the cancer.

In another aspect, described herein is an array for detecting microsatellite instability in a cancer, the array comprising nucleic acids that permit the detection of microsatellite mutation in a set of microsatellite repeat marker sequences in the cancer, wherein the nucleic acids are linked to a solid support.

In one embodiment of any of the aspects, the set of microsatellite repeat markers comprises a plurality of up to 800 of the microsatellites set out herein or in Appendix A of U.S. Provisional Application No. 63/044,029 filed Jun. 25, 2020, the contents of which are incorporated herein by reference in their entirety.

In some embodiments of any of the aspects, when the cancer is colon adenocarcinoma (COAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 1. In some embodiments of any of the aspects, when the cancer is esophageal carcinoma (ESCA), the set of microsatellite repeat marker sequences comprises a plurality up to 503 of the microsatellites set out in Table 2. In some embodiments of any of the aspects, when the cancer is glioblastoma multiforme (GBM), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 3. In some embodiments of any of the aspects, when the cancer is lung adenocarcinoma (LUAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 4. In some embodiments of any of the aspects, when the cancer is lung squamous cell carcinoma (LUSC), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 5. In some embodiments of any of the aspects, when the cancer is rectum adenocarcinoma (READ), the set of microsatellite repeat marker sequences comprises a plurality up to 501 of the microsatellites set out in Table 6. In some embodiments of any of the aspects, when the cancer is stomach adenocarcinoma (STAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 7. In some embodiments of any of the aspects, when the cancer is brain lower grade glioma (LGG), the set of microsatellite repeat marker sequences comprises a plurality up to 266 of the microsatellites set out in Table 8. In some embodiments of any of the aspects, when the cancer is prostate adenocarcinoma (PRAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 9. In some embodiments of any of the aspects, when the cancer is cervical squamous cell carcinoma (CESC), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 10. In some embodiments of any of the aspects, when the cancer is lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), the set of microsatellite repeat marker sequences comprises a plurality up to 212 of the microsatellites set out in Table 11. In some embodiments of any of the aspects, when the cancer is uterine corpus endometrial carcinoma (UCEC), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 12. In some embodiments of any of the aspects, when the cancer is kidney renal clear cell carcinoma (KIRC), the set of microsatellite repeat marker sequences comprises a plurality up to 508 of the microsatellites set out in Table 13. In some embodiments of any of the aspects, when the cancer is breast invasive carcinoma (BRCA), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 14A. In some embodiments of any of the aspects, when the cancer is breast invasive carcinoma (BRCA), the set of microsatellite repeat marker sequences comprises a plurality up to 800 of the microsatellites set out in Tables 14A-14B. In some embodiments of any of the aspects, when the cancer is uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or stomach adenocarcinoma (STAD), the set of microsatellite repeat marker sequences comprises a plurality up to 37 of the microsatellites set out in Table 21.

In another embodiment of any of the aspects, cancer that exhibits greater than or equal to the threshold number of mutations for that tumor type in the set is determined to be MSI-H, and cancer that exhibits fewer than the threshold number of mutations for that tumor type in the set, the subject's cancer is determined to be microsatellite stable or not MSI-H.

In some embodiments of any of the aspects, when the cancer is colon adenocarcinoma (COAD), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 1 and the threshold number is 50%. In some embodiments of any of the aspects, when the cancer is esophageal carcinoma (ESCA), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 2 and the threshold number is 50%. In some embodiments of any of the aspects, when the cancer is glioblastoma multiforme (GBM), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 3 and the threshold number is 50%. In some embodiments of any of the aspects, when the cancer is lung adenocarcinoma (LUAD), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 4 and the threshold number is 50%. In some embodiments of any of the aspects, when the cancer is lung squamous cell carcinoma (LUSC), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 5 and the threshold number is 50%. In some embodiments of any of the aspects, when the cancer is rectum adenocarcinoma (READ), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 6 and the threshold number is 50%. In some embodiments of any of the aspects, when the cancer is stomach adenocarcinoma (STAD), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 7 and the threshold number is 25%. In some embodiments of any of the aspects, when the cancer is brain lower grade glioma (LGG), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 8 and the threshold number is 12.5%. In some embodiments of any of the aspects, when the cancer is prostate adenocarcinoma (PRAD), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 9 and the threshold number is 16.7%. In some embodiments of any of the aspects, when the cancer is cervical squamous cell carcinoma (CESC), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 10 and the threshold number is 45.8%. In some embodiments of any of the aspects, when the cancer is lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 11 and the threshold number is 25%. In some embodiments of any of the aspects, when the cancer is uterine corpus endometrial carcinoma (UCEC), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 12 and the threshold number is 12.9%. In some embodiments of any of the aspects, when the cancer is kidney renal clear cell carcinoma (KIRC), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 13 and the threshold number is 7.5%. In some embodiments of any of the aspects, when the cancer is breast invasive carcinoma (BRCA), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 14A and the threshold number is 3.6%. In some embodiments of any of the aspects, when the cancer is uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or stomach adenocarcinoma (STAD), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 21 and the threshold number is at least 12.9% (e.g., 12.9%, 25%, 50%).

In another embodiment of any of the aspects, the quantitative model is selected from a continuous measure, regression or weighted scoring of markers, a combinatorial or decision-tree model, and a machine learning model. In another embodiment of any of the aspects, the quantitative model comprises a random-forest model or a deep neural network machine learning model.

In some embodiments of any of the aspects, information from individual markers can be combined to produce a final measure, non-limiting examples of which include a classification, score, probability, or prediction of MSI (e.g., stable, unstable, intermediate, indeterminate, or a continuous measure or probability of instability). Methods for analyzing information from individual markers to produce such a measure can include but are not limited to: additive scoring systems with or without use of weighting of individual markers (see e.g., Mehta et al. J Clin Epidemiol. 2016 November, 79:22-28; Austin et al. Stat Med. 2016, 35(22):4056-4072, published correction appears in Stat Med. 2018 Apr. 15, 37(8):1405; Avila et al. BMC Res Notes 8, 612 (2015)); traditional statistical methods such as linear, logistic, or Lasso regression (see e.g., Nick and Campbell (2007) Logistic Regression, in: Ambrosius W. T. (eds) Topics in Biostatistics, Methods in Molecular Biology™, vol 404, Humana Press; Eberly (2007) Multiple Linear Regression, in: Ambrosius W. T. (eds) Topics in Biostatistics, Methods in Molecular Biology™, vol 404, Humana Press; Tibshirani, Journal of the Royal Statistical Society, Series B (Methodological), vol. 58, no. 1, 1996, pp. 267-288); inverse probability-weighted estimation (see e.g., Curtis et al. Medical Care, vol. 45, no. 10, 2007, pp. 5103-5107); Bayesian methods (see e.g., Eberly 2007, supra); classifiers such as support vector machine (see e.g., Cortes and Vapnik, Mach Learn 20, 273-297 (1995)); principal component analysis (see e.g., Lever et al. Nat Methods 14, 641-642 (2017)); hierarchical clustering (see e.g., Rokach et al. Data mining and knowledge discovery handbook, Springer US, 2005, 321-352); decision trees (see e.g., Safavian and Landgrebe, IEEE Transactions on Systems, Man, and Cybernetics, vol. 21, no. 3, pp. 660-674, May-June 1991); random forest models (see e.g., Breiman, Random Forests. Machine Learning 45, 5-32 (2001)); gradient boosting methods (see e.g., Hastie et al. (2009), “10. Boosting and Additive Trees,” The Elements of Statistical Learning (2nd ed.), ISBN 978-0-387-84857-0, New York: Springer, pp. 337-384; Kobayashi and Yoshida, Environ Res. 2021 May, 196:110363); or machine learning approaches such as deep neural networks (see e.g., LeCun et al. Nature 521, 436-444 (2015)). In some embodiments of any of the aspects, missing data for individual markers can be handled intrinsically by models capable of utilizing missing data or can be accounted for using supplementary approaches to account for missing data such as imputation (see e.g., Eberly 2007, supra). The contents of each of the abovementioned references are incorporated herein by reference in their entireties.

In another embodiment of any of the aspects, the quantitative model evaluates or incorporates consideration of one or more test characteristics selected from the group consisting of sensitivity, accuracy, correlation, probability, specificity, false-positive rate, false negative rate, positive predictive value, negative predictive value and area under the receiver-operator characteristic (AUROC). In another embodiment of any of the aspects, the continuous measure comprises the proportion of unmutated or stable loci to mutated or unstable loci detected in the set.

In another embodiment of any of the aspects, thresholds for the one or more test characteristics indicative of MSI-H or MSS are defined within parameters of the known test characteristics for a given clinical application. In another embodiment of any of the aspects, the processing of MSI-H or MSS is determined by a threshold value for the set of microsatellite marker sequences. In another embodiment of any of the aspects, the threshold for the set of microsatellite marker sequences is determined using the percentage of mutated microsatellite markers in the set to calculate the area under the receiver operating characteristic (AUROC). In another embodiment of any of the aspects, the smallest number of markers in the set necessary to reach a selected AUROC value is the threshold. In another embodiment of any of the aspects, the selected AUROC value is a value between 0.6 and 0.99, inclusive. In another embodiment of any of the aspects, the selected AUROC value is 0.9 or more.

In another embodiment of any of the aspects, the set of microsatellite repeat marker sequences comprises a plurality up to 200 of the sequences set out in the respective Table for the subject's cancer type. In another embodiment of any of the aspects, the set of microsatellite repeat marker sequences comprises a plurality up to 300 of the sequences set out in the respective Table for the subject's cancer type. In another embodiment of any of the aspects, the set of microsatellite repeat marker sequences comprises a plurality up to the first 100 of the sequences set out in the respective Table for the subject's cancer type. In another embodiment of any of the aspects, the set of microsatellite repeat marker sequences comprises a plurality up to the first 200 of the sequences set out in the respective Table for the subject's cancer type. In another embodiment of any of the aspects, the set of microsatellite repeat marker sequences comprises a plurality up to the first 300 of the sequences set out in the respective Table for the subject's cancer type.

In another embodiment of any of the aspects, the checkpoint inhibitor immunotherapy comprises a checkpoint inhibitor antibody. In another embodiment of any of the aspects, the checkpoint inhibitor immunotherapy is an inhibitor of a checkpoint molecule selected from the group consisting of: PD-1 or PD-L1, CTLA4, Adenosine A2A receptor (A2AR), CD276, CD39, CD73, B7 family immune checkpoint molecules, V-set domain-containing T-cell activation inhibitor 1 (B7H4), B and T Lymphocyte Attenuator (BTLA), Indoleamine 2,3-dioxygenase (IDO), Killer-cell Immunoglobulin-like Receptor (KIR), Lymphocyte Activation Gene-3 (LAG3), nicotinamide adenine dinucleotide phosphate NADPH oxidase isoform 2 (NOX2), T-cell Immunoglobulin domain and Mucin domain 3 (TIM-3), T cell immunoreceptor with Ig and ITIM domains (TIGIT), V-domain Ig suppressor of T cell activation (VISTA), and Sialic acid-binding immunoglobulin-type lectin 7 (SIGLEC7). In another embodiment of any of the aspects, the checkpoint inhibitor is selected from the group consisting of pembrolizumab (Keytruda®), nivolumab (Opdivo®), cemiplimab (Libtayo®), spartalizumab, camrelizumab, sintilimab, tislelizumab, toripalimab, dostarlimab, INVMGA00012, AMP-224, AMP-514, atezolizumab (Tecentriq®), avelumab (Bavencio®), survalumab (Imfinzi®), KN035, CK-301, AUNP12, CA-170, BMS-986189, and ipilimumab (Yervoy®)

In another embodiment of any of the aspects, the non-checkpoint inhibitor cancer therapy comprises one or more of angiostatin K1-3, DL-α-Difluoromethyl-ornithine, endostatin, fumagillin, genistein, minocycline, staurosporine, and (±)-thalidomide; a DNA intercalator/cross-linker, such as Bleomycin, Carboplatin, Carmustine, Chlorambucil, Cyclophosphamide, cis-Diammineplatinum(II) dichloride (Cisplatin), Melphalan, Mitoxantrone, and Oxaliplatin; a DNA synthesis inhibitor, such as (±)-Amethopterin (Methotrexate), 3-Amino-1,2,4-benzotriazine 1,4-dioxide, Aminopterin, Cytosine β-D-arabinofuranoside, 5-Fluoro-5′-deoxyuridine, 5-Fluorouracil, Ganciclovir, Hydroxyurea, and Mitomycin C; a DNA-RNA transcription regulator, such as Actinomycin D, Daunorubicin, Doxorubicin, Homoharringtonine, and Idarubicin; an enzyme inhibitor, such as S(+)-Camptothecin, Curcumin, (−)-Deguelin, 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside, Etoposide, Formestane, Fostriecin, Hispidin, 2-Imino-1-imidazoli-dineacetic acid (Cyclocreatine), Mevinolin, Trichostatin A, Tyrphostin AG 34, and Tyrphostin AG 879; a gene regulator, such as 5-Aza-2′-deoxycytidine, 5-Azacytidine, Cholecalciferol (Vitamin D3), 4-Hydroxytamoxifen, Melatonin, Mifepristone, Raloxifene, all trans-Retinal (Vitamin A aldehyde), Retinoic acid, all trans (Vitamin A acid), 9-cis-Retinoic Acid, 13-cis-Retinoic acid, Retinol (Vitamin A), Tamoxifen, and Troglitazone; a microtubule inhibitor, such as Colchicine, Dolastatin 15, Nocodazole, Paclitaxel, Podophyllotoxin, Rhizoxin, Vinblastine, Vincristine, Vindesine, and Vinorelbine (Navelbine); a neoantigen; and an unclassified antitumor agent, such as 17-(Allylamino)-17-demethoxygeldanamycin, 4-Amino-1,8-naphthalimide, Apigenin, Brefeldin A, Cimetidine, Dichloromethylene-diphosphonic acid, Leuprolide (Leuprorelin), Luteinizing Hormone-Releasing Hormone, Pifithrin-α, Rapamycin, Sex hormone-binding globulin, Thapsigargin, and Urinary trypsin inhibitor fragment (Bikunin), Vemurafenib (Zelboraf®) imatinib mesylate (Gleevec®), erlotinib (Tarceva®), gefitinib (Iressa®), Vismodegib (Erivedge™), 90Y-ibritumomab tiuxetan, regorafenib (Stivarga®), sunitinib (Sutent®), Denosumab (Xgeva®), sorafenib (Nexavar®), pazopanib (Votrient®), axitinib (Inlyta®), dasatinib (Sprycel®), nilotinib (Tasigna®), bosutinib (Bosulif®), ofatumumab (Arzerra®), obinutuzumab (Gazyva™), ibrutinib (Imbruvica™), idelalisib (Zydelig®), crizotinib (Xalkori®), erlotinib (Tarceva®), afatinib dimaleate (Gilotrif®), ceritinib (LDK378/Zykadia), ibritumomab tiuxetan (Zevalin®), brentuximab vedotin (Adcetris®), bortezomib (Velcade®), siltuximab (Sylvant™), trametinib (Mekinist®), dabrafenib (Tafinlar®), a targeted therapy such as toremifene (Fareston®), fulvestrant (Faslodex®), anastrozole (Arimidex®), exemestane (Aromasin®), letrozole (Ferrara®), ziv-aflibercept (Zaltrap®), Alitretinoin (Panretin®), temsirolimus (Torisel®), Tretinoin (Vesanoid®), denileukin diftitox (Ontak®), vorinostat (Zolinza®), romidepsin (Istodax®), bexarotene (Targretin®), pralatrexate (Folotyn®), lenaliomide (Revlimid®), belinostat (Beleodaq™), lenaliomide (Revlimid®), pomalidomide (Pomalyst®), Cabazitaxel (Jevtana®), enzalutamide (Xtandi®), abiraterone acetate (Zytiga®), radium 223 chloride (Xofigo®), or everolimus (Afinitor®), an epigenetic targeted drug such as HDAC inhibitors, azacitidine (Vidaza®), decitabine (Dacogen®), vorinostat (Zolinza®), romidepsin (Istodax®), ruxolitinib (Jakafi®), kinase inhibitors, DNA methyltransferase inhibitors, histone demethylase inhibitors, or histone methylation inhibitors, and any derivative thereof.

In another embodiment of any of the aspects, assaying loci in the defined set of microsatellite repeat marker sequences in cells of the subject's cancer for mutation comprises polynucleotide sequencing, measurement of total mutational burden, immunohistochemical analysis, and/or polymerase chain reaction. In another embodiment of any of the aspect, polynucleotide sequencing comprises whole genome sequencing, whole exome sequencing, or targeted gene capture sequencing.

In another embodiment of any of the aspects, microsatellite mutations correspond to those identified in reference human genome GRCh37/hg19 translated to a different build of the human reference genome.

In another embodiment of any of the aspects, the kit comprises an array of reagents that permit the detection of microsatellite mutation on a solid support. In another embodiment of any of the aspects, the reagents comprise PCR primers that permit amplification of members of the set of microsatellite repeat marker sequences.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a dot plot showing the relative burden of microsatellite instability events across cancer types. Percentage of total microsatellite loci found to be mutated are reported per tumor specimen, as stratified by cancer type. Each point corresponds to an individual tumor, and its coloration indicates the corresponding MSI classification. TCGA abbreviations for cancer types are as described in the Table 16 footnote.

FIG. 2 is a heatmap showing that informative markers for diagnosing MSI vary across cancer types. The 2,000 most informative microsatellites (rows) for discriminating MSI positive from MSI negative tumors from each of the indicated cancer types (columns) are displayed. Heatmap coloration indicates the association of individual loci with the MSI-H phenotype, normalized on a per-cancer type basis from zero (least significant) to one (most significant). Hierarchical clustering of cancer types according to similarity in microsatellite mutation patterns is indicated at top. TCGA abbreviations for cancer types are as described in the Table 16 footnote.

FIG. 3A-3B is a series of line graphs showing the performance characteristics of variously sized tissue-specific panels for MSI diagnosis. Area under the receiver operating characteristic (AUROC) is shown as a function of the number of most highly informative markers examined for various cancer types. FIG. 3A shows the results for the training set from which informative microsatellites were initially identified. FIG. 3B shows the results for an independent validation set for each tumor type. TCGA abbreviations for cancer types are as described in the Table 16 footnote.

FIG. 4A-4C shows the properties of informative microsatellites. The ridgeline plots show the density of −log₁₀ transformed p values for specified features among microsatellites that are informative for diagnosing MSI. A shift to the right in the placement of distributions corresponds to increased association with locus instability in MSI. FIG. 4A shows repeat type. FIG. 4B shows genomic context. FIG. 4C shows the number of repeats in a microsatellite.

FIG. 5 shows the relative burden of microsatellite instability events across cancer types, inferred from whole genome sequence data. Percentage of total microsatellite loci found to be mutated are reported per tumor specimen, as stratified by cancer type. Each point corresponds to an individual tumor, and its shade of grey indicates the corresponding MSI classification. TCGA abbreviations for cancer types are as described in the Table 16 footnote.

DETAILED DESCRIPTION

The methods and compositions described herein relate, in part, to the discovery of microsatellite repeat marker sequences that predict whether a subject will respond to checkpoint inhibitor immunotherapy for each cancer type. The methods comprise assaying mutation status for a set of microsatellite repeat marker sequences in cells of the subject's cancer, wherein when the set of microsatellites exhibits mutation at or above a threshold number of microsatellites in the set, the subject's cancer is determined to exhibit high microsatellite instability (MSI-H). The microsatellite repeat marker sequences for each cancer type that are most predictive of a subject's response to checkpoint inhibitor immunotherapy are provided below, e.g., in Tables 1-15. In Tables 1-15, chromosome is abbreviated as “ch.” The chromosome sequences of GRCh37/hg19 (also referred to herein as hg37) can be found at the following accession numbers indicated in Table 18 below.

TABLE 18 GRCh37/hg19 Reference Sequences; the indicated chromosome sequences are incorporated herein by reference in their entireties Molecule name GenBank sequence RefSeq sequence Chromosome 1 CM000663.1 NC_000001.10 Chromosome 2 CM000664.1 NC_000002.11 Chromosome 3 CM000665.1 NC_000003.11 Chromosome 4 CM000666.1 NC_000004.11 Chromosome 5 CM000667.1 NC_000005.9 Chromosome 6 CM000668.1 NC_000006.11 Chromosome 7 CM000669.1 NC_000007.13 Chromosome 8 CM000670.1 NC_000008.10 Chromosome 9 CM000671.1 NC_000009.11 Chromosome 10 CM000672.1 NC_000010.10 Chromosome 11 CM000673.1 NC_000011.9 Chromosome 12 CM000674.1 NC_000012.11 Chromosome 13 CM000675.1 NC_000013.10 Chromosome 14 CM000676.1 NC_000014.8 Chromosome 15 CM000677.1 NC_000015.9 Chromosome 16 CM000678.1 NC_000016.9 Chromosome 17 CM000679.1 NC_000017.10 Chromosome 18 CM000680.1 NC_000018.9 Chromosome 19 CM000681.1 NC_000019.9 Chromosome 20 CM000682.1 NC_000020.10 Chromosome 21 CM000683.1 NC_000021.8 Chromosome 22 CM000684.1 NC_000022.10 Chromosome X CM000685.1 NC_000023.10 Chromosome Y CM000686.1 NC_000024.9

In some embodiments of any of the aspects, a set of microsatellite repeat marker sequences are selected from the respective Table for the subject's cancer type (e.g., at least one of Tables 1-15 or Table 21). In some embodiments of any of the aspects, a set of microsatellite repeat marker sequences comprises a plurality up to 800 of the microsatellites set out in the respective Table for the subject's cancer type (e.g., at least one of Tables 1-15 or Table 21). In some embodiments of any of the aspects, a set of microsatellite repeat marker sequences comprises a plurality of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, at least 50, at least 51, at least 52, at least 53, at least 54, at least 55, at least 56, at least 57, at least 58, at least 59, at least 60, at least 61, at least 62, at least 63, at least 64, at least 65, at least 66, at least 67, at least 68, at least 69, at least 70, at least 71, at least 72, at least 73, at least 74, at least 75, at least 76, at least 77, at least 78, at least 79, at least 80, at least 81, at least 82, at least 83, at least 84, at least 85, at least 86, at least 87, at least 88, at least 89, at least 90, at least 91, at least 92, at least 93, at least 94, at least 95, at least 96, at least 97, at least 98, at least 99, at least 100, at least 101, at least 102, at least 103, at least 104, at least 105, at least 106, at least 107, at least 108, at least 109, at least 110, at least 111, at least 112, at least 113, at least 114, at least 115, at least 116, at least 117, at least 118, at least 119, at least 120, at least 121, at least 122, at least 123, at least 124, at least 125, at least 126, at least 127, at least 128, at least 129, at least 130, at least 131, at least 132, at least 133, at least 134, at least 135, at least 136, at least 137, at least 138, at least 139, at least 140, at least 141, at least 142, at least 143, at least 144, at least 145, at least 146, at least 147, at least 148, at least 149, at least 150, at least 151, at least 152, at least 153, at least 154, at least 155, at least 156, at least 157, at least 158, at least 159, at least 160, at least 161, at least 162, at least 163, at least 164, at least 165, at least 166, at least 167, at least 168, at least 169, at least 170, at least 171, at least 172, at least 173, at least 174, at least 175, at least 176, at least 177, at least 178, at least 179, at least 180, at least 181, at least 182, at least 183, at least 184, at least 185, at least 186, at least 187, at least 188, at least 189, at least 190, at least 191, at least 192, at least 193, at least 194, at least 195, at least 196, at least 197, at least 198, at least 199, at least 200, at least 201, at least 202, at least 203, at least 204, at least 205, at least 206, at least 207, at least 208, at least 209, at least 210, at least 211, at least 212, at least 213, at least 214, at least 215, at least 216, at least 217, at least 218, at least 219, at least 220, at least 221, at least 222, at least 223, at least 224, at least 225, at least 226, at least 227, at least 228, at least 229, at least 230, at least 231, at least 232, at least 233, at least 234, at least 235, at least 236, at least 237, at least 238, at least 239, at least 240, at least 241, at least 242, at least 243, at least 244, at least 245, at least 246, at least 247, at least 248, at least 249, at least 250, at least 251, at least 252, at least 253, at least 254, at least 255, at least 256, at least 257, at least 258, at least 259, at least 260, at least 261, at least 262, at least 263, at least 264, at least 265, at least 266, at least 267, at least 268, at least 269, at least 270, at least 271, at least 272, at least 273, at least 274, at least 275, at least 276, at least 277, at least 278, at least 279, at least 280, at least 281, at least 282, at least 283, at least 284, at least 285, at least 286, at least 287, at least 288, at least 289, at least 290, at least 291, at least 292, at least 293, at least 294, at least 295, at least 296, at least 297, at least 298, at least 299, at least 300, at least 301, at least 302, at least 303, at least 304, at least 305, at least 306, at least 307, at least 308, at least 309, at least 310, at least 311, at least 312, at least 313, at least 314, at least 315, at least 316, at least 317, at least 318, at least 319, at least 320, at least 321, at least 322, at least 323, at least 324, at least 325, at least 326, at least 327, at least 328, at least 329, at least 330, at least 331, at least 332, at least 333, at least 334, at least 335, at least 336, at least 337, at least 338, at least 339, at least 340, at least 341, at least 342, at least 343, at least 344, at least 345, at least 346, at least 347, at least 348, at least 349, at least 350, at least 351, at least 352, at least 353, at least 354, at least 355, at least 356, at least 357, at least 358, at least 359, at least 360, at least 361, at least 362, at least 363, at least 364, at least 365, at least 366, at least 367, at least 368, at least 369, at least 370, at least 371, at least 372, at least 373, at least 374, at least 375, at least 376, at least 377, at least 378, at least 379, at least 380, at least 381, at least 382, at least 383, at least 384, at least 385, at least 386, at least 387, at least 388, at least 389, at least 390, at least 391, at least 392, at least 393, at least 394, at least 395, at least 396, at least 397, at least 398, at least 399, at least 400, at least 401, at least 402, at least 403, at least 404, at least 405, at least 406, at least 407, at least 408, at least 409, at least 410, at least 411, at least 412, at least 413, at least 414, at least 415, at least 416, at least 417, at least 418, at least 419, at least 420, at least 421, at least 422, at least 423, at least 424, at least 425, at least 426, at least 427, at least 428, at least 429, at least 430, at least 431, at least 432, at least 433, at least 434, at least 435, at least 436, at least 437, at least 438, at least 439, at least 440, at least 441, at least 442, at least 443, at least 444, at least 445, at least 446, at least 447, at least 448, at least 449, at least 450, at least 451, at least 452, at least 453, at least 454, at least 455, at least 456, at least 457, at least 458, at least 459, at least 460, at least 461, at least 462, at least 463, at least 464, at least 465, at least 466, at least 467, at least 468, at least 469, at least 470, at least 471, at least 472, at least 473, at least 474, at least 475, at least 476, at least 477, at least 478, at least 479, at least 480, at least 481, at least 482, at least 483, at least 484, at least 485, at least 486, at least 487, at least 488, at least 489, at least 490, at least 491, at least 492, at least 493, at least 494, at least 495, at least 496, at least 497, at least 498, at least 499, at least 500, at least 501, at least 502, at least 503, at least 504, at least 505, at least 506, at least 507, or at least 508, at least 509, at least 510, at least 515, at least 520, at least 525, at least 530, at least 535, at least 540, at least 545, at least 550, at least 555, at least 560, at least 565, at least 570, at least 575, at least 580, at least 585, at least 590, at least 595, at least 600, at least 605, at least 610, at least 615, at least 620, at least 625, at least 630, at least 635, at least 640, at least 645, at least 650, at least 655, at least 660, at least 665, at least 670, at least 675, at least 680, at least 685, at least 690, at least 695, at least 700, at least 705, at least 710, at least 715, at least 720, at least 725, at least 730, at least 735, at least 740, at least 745, at least 750, at least 755, at least 760, at least 765, at least 770, at least 775, at least 780, at least 785, at least 790, at least 795, or at least 800 or more of the microsatellites set out in the respective Table for the subject's cancer type (e.g., at least one of Tables 1-15 or Table 21).

In some embodiments of any of the aspects, a set of microsatellite repeat marker sequences comprises a plurality of at most 1, at most 2, at most 3, at most 4, at most 5, at most 6, at most 7, at most 8, at most 9, at most 10, at most 11, at most 12, at most 13, at most 14, at most 15, at most 16, at most 17, at most 18, at most 19, at most 20, at most 21, at most 22, at most 23, at most 24, at most 25, at most 26, at most 27, at most 28, at most 29, at most 30, at most 31, at most 32, at most 33, at most 34, at most 35, at most 36, at most 37, at most 38, at most 39, at most 40, at most 41, at most 42, at most 43, at most 44, at most 45, at most 46, at most 47, at most 48, at most 49, at most 50, at most 51, at most 52, at most 53, at most 54, at most 55, at most 56, at most 57, at most 58, at most 59, at most 60, at most 61, at most 62, at most 63, at most 64, at most 65, at most 66, at most 67, at most 68, at most 69, at most 70, at most 71, at most 72, at most 73, at most 74, at most 75, at most 76, at most 77, at most 78, at most 79, at most 80, at most 81, at most 82, at most 83, at most 84, at most 85, at most 86, at most 87, at most 88, at most 89, at most 90, at most 91, at most 92, at most 93, at most 94, at most 95, at most 96, at most 97, at most 98, at most 99, at most 100, at most 101, at most 102, at most 103, at most 104, at most 105, at most 106, at most 107, at most 108, at most 109, at most 110, at most 111, at most 112, at most 113, at most 114, at most 115, at most 116, at most 117, at most 118, at most 119, at most 120, at most 121, at most 122, at most 123, at most 124, at most 125, at most 126, at most 127, at most 128, at most 129, at most 130, at most 131, at most 132, at most 133, at most 134, at most 135, at most 136, at most 137, at most 138, at most 139, at most 140, at most 141, at most 142, at most 143, at most 144, at most 145, at most 146, at most 147, at most 148, at most 149, at most 150, at most 151, at most 152, at most 153, at most 154, at most 155, at most 156, at most 157, at most 158, at most 159, at most 160, at most 161, at most 162, at most 163, at most 164, at most 165, at most 166, at most 167, at most 168, at most 169, at most 170, at most 171, at most 172, at most 173, at most 174, at most 175, at most 176, at most 177, at most 178, at most 179, at most 180, at most 181, at most 182, at most 183, at most 184, at most 185, at most 186, at most 187, at most 188, at most 189, at most 190, at most 191, at most 192, at most 193, at most 194, at most 195, at most 196, at most 197, at most 198, at most 199, at most 200, at most 201, at most 202, at most 203, at most 204, at most 205, at most 206, at most 207, at most 208, at most 209, at most 210, at most 211, at most 212, at most 213, at most 214, at most 215, at most 216, at most 217, at most 218, at most 219, at most 220, at most 221, at most 222, at most 223, at most 224, at most 225, at most 226, at most 227, at most 228, at most 229, at most 230, at most 231, at most 232, at most 233, at most 234, at most 235, at most 236, at most 237, at most 238, at most 239, at most 240, at most 241, at most 242, at most 243, at most 244, at most 245, at most 246, at most 247, at most 248, at most 249, at most 250, at most 251, at most 252, at most 253, at most 254, at most 255, at most 256, at most 257, at most 258, at most 259, at most 260, at most 261, at most 262, at most 263, at most 264, at most 265, at most 266, at most 267, at most 268, at most 269, at most 270, at most 271, at most 272, at most 273, at most 274, at most 275, at most 276, at most 277, at most 278, at most 279, at most 280, at most 281, at most 282, at most 283, at most 284, at most 285, at most 286, at most 287, at most 288, at most 289, at most 290, at most 291, at most 292, at most 293, at most 294, at most 295, at most 296, at most 297, at most 298, at most 299, at most 300, at most 301, at most 302, at most 303, at most 304, at most 305, at most 306, at most 307, at most 308, at most 309, at most 310, at most 311, at most 312, at most 313, at most 314, at most 315, at most 316, at most 317, at most 318, at most 319, at most 320, at most 321, at most 322, at most 323, at most 324, at most 325, at most 326, at most 327, at most 328, at most 329, at most 330, at most 331, at most 332, at most 333, at most 334, at most 335, at most 336, at most 337, at most 338, at most 339, at most 340, at most 341, at most 342, at most 343, at most 344, at most 345, at most 346, at most 347, at most 348, at most 349, at most 350, at most 351, at most 352, at most 353, at most 354, at most 355, at most 356, at most 357, at most 358, at most 359, at most 360, at most 361, at most 362, at most 363, at most 364, at most 365, at most 366, at most 367, at most 368, at most 369, at most 370, at most 371, at most 372, at most 373, at most 374, at most 375, at most 376, at most 377, at most 378, at most 379, at most 380, at most 381, at most 382, at most 383, at most 384, at most 385, at most 386, at most 387, at most 388, at most 389, at most 390, at most 391, at most 392, at most 393, at most 394, at most 395, at most 396, at most 397, at most 398, at most 399, at most 400, at most 401, at most 402, at most 403, at most 404, at most 405, at most 406, at most 407, at most 408, at most 409, at most 410, at most 411, at most 412, at most 413, at most 414, at most 415, at most 416, at most 417, at most 418, at most 419, at most 420, at most 421, at most 422, at most 423, at most 424, at most 425, at most 426, at most 427, at most 428, at most 429, at most 430, at most 431, at most 432, at most 433, at most 434, at most 435, at most 436, at most 437, at most 438, at most 439, at most 440, at most 441, at most 442, at most 443, at most 444, at most 445, at most 446, at most 447, at most 448, at most 449, at most 450, at most 451, at most 452, at most 453, at most 454, at most 455, at most 456, at most 457, at most 458, at most 459, at most 460, at most 461, at most 462, at most 463, at most 464, at most 465, at most 466, at most 467, at most 468, at most 469, at most 470, at most 471, at most 472, at most 473, at most 474, at most 475, at most 476, at most 477, at most 478, at most 479, at most 480, at most 481, at most 482, at most 483, at most 484, at most 485, at most 486, at most 487, at most 488, at most 489, at most 490, at most 491, at most 492, at most 493, at most 494, at most 495, at most 496, at most 497, at most 498, at most 499, at most 500, at most 501, at most 502, at most 503, at most 504, at most 505, at most 506, at most 507, at most 508, at most 509, at most 510, at most 515, at most 520, at most 525, at most 530, at most 535, at most 540, at most 545, at most 550, at most 555, at most 560, at most 565, at most 570, at most 575, at most 580, at most 585, at most 590, at most 595, at most 600, at most 605, at most 610, at most 615, at most 620, at most 625, at most 630, at most 635, at most 640, at most 645, at most 650, at most 655, at most 660, at most 665, at most 670, at most 675, at most 680, at most 685, at most 690, at most 695, at most 700, at most 705, at most 710, at most 715, at most 720, at most 725, at most 730, at most 735, at most 740, at most 745, at most 750, at most 755, at most 760, at most 765, at most 770, at most 775, at most 780, at most 785, at most 790, at most 795, at most 800 of the microsatellites set out in the respective Table for the subject's cancer type (e.g., at least one of Tables 1-15 or Table 21).

The microsatellite repeat marker sequences in Tables 1-15 are listed in rank order; i.e., they are ordered by significance, from the highest significance (i.e., lowest p-value) in the first data row, to the lowest significance (i.e., highest p-value) in the last data row. In some embodiments of any of the aspects, the set of microsatellite repeat marker sequences comprises a plurality up to the first 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, or 800 or more of the sequences set out in the respective Table for the subject's cancer type e.g., at least one of Tables 1-15).

In some embodiments of any of the aspects, the set of microsatellite repeat marker sequences comprises a plurality comprising sequences, each with a p-value of no more than 1E-48, no more than 1E-47, no more than 1E-46, no more than 1E-45, no more than 1E-44, no more than 1E-43, no more than 1E-42, no more than 1E-41, no more than 1E-40, no more than 1E-39, no more than 1E-38, no more than 1E-37, no more than 1E-36, no more than 1E-35, no more than 1E-34, no more than 1E-33, no more than 1E-32, no more than 1E-31, no more than 1E-30, no more than 1E-29, no more than 1E-28, no more than 1E-27, no more than 1E-26, no more than 1E-25, no more than 1E-24, no more than 1E-23, no more than 1E-22, no more than 1E-21, no more than 1E-20, no more than 1E-19, no more than 1E-18, no more than 1E-17, no more than 1E-16, no more than 1E-15, no more than 1E-14, no more than 1E-13, no more than 1E-12, no more than 1E-11, no more than 1E-10, no more than 1E-9, no more than 1E-8, no more than 1E-7, no more than 1E-6, no more than 1E-5, no more than 1E-4, no more than 1E-3, no more than 0.01, no more than 0.02, no more than 0.03, no more than 0.04, or no more than 0.05, as set out in the respective Table for the subject's cancer type e.g., at least one of Tables 1-15).

TABLE 1 Microsatellite Repeat Marker Sequences for Colon Adenocarcinoma (COAD). TABLE 1 - COAD ch start_pos end_pos COAD (hg37) (hg37) (hg37) gene p-value 9 133498229 133498245 FUBP3 1.97444E−42 22 30051705 30051722 NF2  4.2723E−40 17 29508819 29508836 NF1 7.41122E−39 18 649879 649895 TYMSOS(NM_001012716: c.*120_*104del0) 1.18183E−38 13 28133956 28133972 LNX2 5.27268E−38 6 111329221 111329239 RPF2  6.2912E−38 1 33402334 33402352 RNF19B(NM_001127361: c.*555_*537del0, 7.77278E−38 NM_153341: c.*73_*55del0, NM_001300826: c.*73_*55del0) 7 92900502 92900527 CCDC132 1.12934E−37 10 112360315 112360333 SMC3 1.17805E−37 6 89638988 89639004 RNGTT  1.3471E−37 5 86679495 86679514 RASA1 1.90078E−37 4 146031236 146031253 ABCE1 3.46974E−37 2 99936265 99936280 TXNDC9 1.18581E−36 3 32571823 32571841 DYNC1LI1 1.85388E−36 X 106092450 106092473 TBCID8B 2.91268E−36 1 32381592 32381607 PTP4A2 5.75413E−36 4 115586972 115586988 UGT8 6.55335E−36 2 62063093 62063111 FAM161A 6.90573E−36 6 32147291 32147312 RNF5P1 8.98174E−36 16 75674252 75674271 KARS  1.567E−35 5 172578549 172578567 BNIP1 5.32873E−35 5 94842718 94842730 TTC37 1.08708E−34 12 110834030 110834049 ANAPC7 1.84502E−34 14 73959703 73959720 C14orf169(NM_024644: c.*56_*73del0)  2.1326E−34 2 15536509 15536532 NBAS 2.20429E−34 1 94964139 94964155 ABCD3 3.83708E−34 20 35695535 35695562 RBL1 4.26031E−34 13 79216356 79216381 RNF219 6.25174E−34 5 172421760 172421776 ATP6V0E1 8.57225E−34 2 48734331 48734349 PPP1R21 1.27747E−33 1 150676674 150676692 HORMAD1 1.37307E−33 3 196088809 196088826 UBXN7 1.58786E−33 8 103287850 103287864 UBR5 1.60937E−33 3 138248009 138248026 CEP70 1.88658E−33 9 30689085 30689104 LINC01242(dist = 280633), ACO1(dist = 1695497) 3.97068E−33 6 157495951 157495966 ARID1B 4.13998E−33 2 74089266 74089281 STAMBP  5.7002E−33 2 61308569 61308585 KIAA1841 8.51011E−33 6 49415351 49415368 MUT 8.71316E−33 1 47123898 47123914 ATPAF1 2.42202E−32 1 113159364 113159384 ST7L 2.59998E−32 6 36452603 36452620 KCTD20 2.82618E−32 5 50122645 50122660 PARP8 2.91483E−32 14 59787325 59787338 DAAM1 3.69262E−32 2 201778717 201778733 ORC2  3.824E−32 1 223156384 223156419 DISP1 4.72047E−32 16 47399670 47399687 ITFG1 6.48005E−32 7 36465606 36465622 ANLN 8.85541E−32 14 58825825 58825847 ARID4A  8.8991E−32 7 54819993 54820005 SEC61G(NM_014302: c.*111_*99del0, 9.41642E−32 NM_001012456: c.*111_*99del0) 21 37706065 37706077 MORC3 1.05742E−31 1 165712555 165712571 TMCO1 1.70961E−31 1 212217944 212217961 DTL 2.36848E−31 2 55883509 55883523 PNPT1 3.31975E−31 16 90141288 90141302 PRDM7 3.78188E−31 1 63044645 63044661 DOCK7 5.63554E−31 X 96171416 96171435 DIAPH2 6.17561E−31 11 110128925 110128941 RDX 7.14912E−31 3 132169705 132169718 DNAJC13 7.16803E−31 8 53543090 53543106 RB1CC1 8.99963E−31 4 128814425 128814449 PLK4 1.82148E−30 3 71008341 71008362 FOXP1(NM_001244816: c._*57_*36del0, 1.84404E−30 NM_001244812: c.*57_*36del0, NM_001244813: c.*57_*36del0, NM_001244808: c.*57_*36del0, NM_001244815: c.*57_*36del0, NM_001244814: c.*57_*36del0, NM_032682: c.*57_*36del0, NM_001244810: c.*57_*36del0) 4 39501722 39501754 MIR1273H 2.16074E−30 9 163927 163943 CBWD1 2.29365E−30 10 30605169 30605182 MTPAP  2.4128E−30 X 18800531 18800548 PPEF1 3.27994E−30 18 19119813 19119828 ESCO1 3.29335E−30 17 30293149 30293164 SUZ12 3.31796E−30 13 103257289 103257311 TPP2 3.66206E−30 2 109371849 109371865 RANBP2 4.87581E−30 12 89853387 89853405 POC1B 5.24509E−30 18 33058318 33058335 INO80C 7.15262E−30 6 100988266 100988280 ASCC3 7.50578E−30 2 61577667 61577680 USP34 7.77574E−30 3 58351660 58351690 PXK 8.33089E−30 14 68582259 68582279 RAD51B 8.94048E−30 1 197053561 197053577 ASPM 9.31752E−30 3 169992958 169992994 PRKCI 9.86781E−30 8 3611416 3611429 CSMD1 1.83694E−29 2 32117217 32117230 MEMO1 1.85212E−29 13 39608335 39608360 PROSER1 1.88642E−29 X 84523274 84523298 ZNF711  2.1074E−29 12 109510086 109510099 USP30 2.14945E−29 15 50596341 50596355 GABPB1 2.77078E−29 12 110006724 110006738 MMAB 2.92762E−29 12 76780051 76780066 OSBPL8 2.92907E−29 4 128812230 128812245 PLK4 3.02816E−29 1 222904869 222904881 BROX 4.84008E−29 12 104714847 104714867 TXNRD1 5.16677E−29 9 125655308 125655324 RC3H2 5.31074E−29 5 36123065 36123135 LMBRD2 5.75649E−29 2 112854563 112854576 TMEM87B 7.87714E−29 2 203676382 203676403 ICA1L 1.02838E−28 4 128817905 128817919 PLK4 1.03158E−28 6 24515330 24515350 ALDH5A1 1.04464E−28 16 15159022 15159039 PDXDC1, RRN3 1.07089E−28 20 35672436 35672456 RBL1  1.7126E−28 8 30933816 30933829 WRN 1.79545E−28 1 117605130 117605145 TTF2 2.02249E−28 7 16676082 16676097 ANKMY2 2.14328E−28 9 133498017 133498047 FUBP3 2.59338E−28 19 54603097 54603118 OSCAR 2.90262E−28 2 172582088 172582125 DYNC1I2 3.16686E−28 2 103343275 103343295 MFSD9  3.5448E−28 6 70840124 70840137 COL19A1 3.86566E−28 2 234916771 234916787 TRPM8 4.34333E−28 5 14485161 14485175 TRIO 4.43695E−28 14 35242702 35242726 BAZ1A 4.48519E−28 16 10567751 10567778 ATF7IP2  5.3796E−28 1 33087567 33087584 ZBTB8OS 5.39418E−28 X 19037666 19037686 GPR64 5.53603E−28 4 76997157 76997173 ART3 5.75346E−28 19 15511205 15511221 AKAP8L 6.00927E−28 2 179548695 179548712 TTN 6.50856E−28 6 20758808 20758822 CDKAL1 7.44263E−28 8 100160282 100160300 VPS13B  7.5375E−28 5 118500981 118501000 DMXL1 9.02536E−28 3 132173004 132173026 DNAJC13  1.1257E−27 3 33626219 33626236 CLASP2 1.17044E−27 1 183481943 183481964 SMG7 1.25607E−27 5 96093391 96093408 CAST 1.38902E−27 20 58497481 58497497 SYCP2(NM_014258: c.-13_-29del0) 1.66216E−27 9 19299209 19299224 DENND4C 1.73078E−27 3 108224685 108224701 MYH15 1.92096E−27 X 48214185 48214200 SSX3 2.22276E−27 3 44846477 44846493 KIF15 2.29722E−27 1 213009178 213009196 SPATA45 2.31418E−27 2 239241445 239241460 TRAF3IP1 2.65192E−27 3 113222099 113222114 SPICE1 2.67655E−27 20 47649496 47649525 ARFGEF2 2.85041E−27 3 111873902 111873917 SLC9C1  3.0073E−27 2 91887905 91887919 LOC654342(dist = 39930), GGT8P(dist = 75449) 3.20197E−27 1 150297334 150297351 PRPF3  3.3667E−27 12 123703074 123703086 MPHOSPH9 3.86064E−27 14 39591613 39591627 GEMIN2 4.36301E−27 10 35314130 35314161 CUL2 4.55769E−27 2 48032740 48032754 MSH6 4.79768E−27 8 96069973 96069988 NDUFAF6 4.87356E−27 1 57249981 57250000 RSPRY1 5.37964E−27 7 74608740 74608754 GTF2IP1, LOC100093631 6.05012E−27 17 28811834 28811848 GOSR1 6.24449E−27 6 11714639 11714665 ADTRP(NM_001143948: c.*72_*46del0, 6.32705E−27 NM_032744: c.*72_*46del0) 12 49091972 49092009 CCNT1 7.01103E−27 2 70456452 70456465 TIA1 8.78721E−27 4 39851058 39851077 PDS5A  1.001E−26 11 108058769 108058785 NPAT 1.01853E−26 5 52358761 52358775 ITGA2 1.22448E−26 2 173435578 173435593 PDK1 1.27764E−26 6 20548763 20548778 CDKAL1 1.30837E−26 18 66367726 66367742 TMX3 1.57507E−26 2 152424933 152424962 NEB 1.75375E−26 3 180320897 180320910 TTC14 1.92782E−26 X 44386435 44386460 FUNDC1 2.11618E−26 15 30875074 30875089 ULK4P1, ULK4P2 2.23317E−26 9 114341239 114341255 PTGR1 2.25943E−26 13 102235764 102235780 ITGBL1 2.28436E−26 16 15162143 15162165 PDXDC1, RRN3 2.44732E−26 2 203079025 203079039 SUMO1 2.47405E−26 4 84519775 84519790 AGPAT9 2.54004E−26 15 55841195 55841209 PYGO1 2.55373E−26 22 41545024 41545039 EP300 2.65914E−26 20 31954819 31954834 CDK5RAP1 2.94342E−26 2 120714401 120714418 PTPN4 2.97068E−26 11 8486375 8486389 STK33  3.0217E−26 2 108520601 108520629 RGPD4(dist = 11601), SLC5A7(dist = 82366) 3.17888E−26 11 59368218 59368235 OSBP 3.72002E−26 20 46266543 46266558 NCOA3 3.73849E−26 2 236877066 236877084 AGAP1 3.85222E−26 11 118884009 118884025 CCDC84 5.08727E−26 1 65099701 65099716 CACHD1 5.33943E−26 14 32142544 32142557 NUBPL 5.75709E−26 14 96770942 96770967 ATG2B 6.43549E−26 16 19063220 19063235 TMC7 6.75772E−26 12 21644428 21644447 RECQL 6.91293E−26 14 53513439 53513452 DDHD1(NM_001160148: c.*47_*34del0, 7.32716E−26 NM_001160147: c.*47_*34del0, NM_030637: c.*47_*34del0) 14 36218039 36218056 RALGAPA1P 8.15888E−26 5 95224700 95224719 ELL2 8.88189E−26 3 71739332 71739345 EIF4E3 9.69231E−26 11 88068256 88068270 CTSC 9.73243E−26 5 41909830 41909846 C5orf51 9.79141E−26 15 82517622 82517671 EFTUD1  1.0184E−25 16 24185815 24185831 PRKCB 1.09299E−25 9 86395372 86395398 GKAP1 1.13366E−25 4 95508108 95508128 PDLIM5 1.13711E−25 3 69112658 69112688 UBA3 1.17295E−25 16 3808052 3808066 CREBBP 1.28767E−25 1 92763091 92763128 GLMN 1.36845E−25 3 121202433 121202476 POLQ 1.37521E−25 8 142161666 142161681 DENND3 1.45121E−25 17 1265304 1265326 YWHAE 1.67543E−25 9 34017005 34017043 UBAP2 1.77445E−25 X 20204548 20204563 RPS6KA3   1.85E−25 4 44691795 44691810 GUF1 1.92631E−25 17 35979746 35979761 DDX52 2.09281E−25 17 54981571 54981588 TRIM25 2.23713E−25 9 116044905 116044921 PRPF4 2.27948E−25 8 109247189 109247210 EIF3E 2.33007E−25 13 48664556 48664569 MED4 2.37233E−25 8 89499214 89499230 MMP16(dist = 159497), LOC101929709(dist = 1230397) 2.53324E−25 20 7921106 7921120 HAO1 2.64395E−25 1 112305406 112305423 DDX20 2.66171E−25 6 152740681 152740695 SYNE1 2.84733E−25 17 19749952 19749969 ULK2  2.863E−25 1 14057425 14057439 PRDM2 2.98632E−25 5 37027560 37027590 NIPBL 3.02598E−25 14 20857306 20857321 TEP1 3.15633E−25 14 36096255 36096278 RALGAPA1P 3.59889E−25 14 60616914 60616937 DHRS7 3.78632E−25 12 48360947 48360961 TMEM106C 3.99918E−25 X 44918221 44918236 KDM6A 4.03992E−25 14 35899480 35899493 NFKBIA(dist = 25520), INSM2(dist = 103755)  4.3902E−25 3 113169372 113169386 SPICE1 4.40181E−25 X 2343183 2343213 DHRSX 4.47914E−25 9 79968285 79968309 VPS13A 4.49841E−25 2 32095023 32095056 MEMO1 4.58282E−25 4 89352469 89352487 HERC6  5.3032E−25 2 64323751 64323763 PELI1 5.65312E−25 11 122928926 122928953 HSPA8 6.23598E−25 7 114303617 114303633 FOXP2 6.55004E−25 5 87494728 87494767 TMEM161B 6.60555E−25 11 14539315 14539332 PSMA1 7.15944E−25 1 159032486 159032497 AIM2 7.94894E−25 1 155701055 155701071 DAP3 8.04399E−25 18 59942586 59942600 KIAA1468 9.06981E−25 6 24412431 24412445 MRS2 1.02893E−24 5 178030941 178030955 CLK4 1.07799E−24 21 27136460 27136473 GABPA 1.13104E−24 12 45771901 45771918 ANO6 1.13312E−24 2 47635523 47635537 MSH2 1.16329E−24 2 120620092 120620108 PTPN4 1.26988E−24 2 111406968 111406984 BUB1 1.28181E−24 2 54146387 54146400 PSME4 1.33261E−24 5 180481216 180481233 BTNL9 1.42643E−24 2 64139831 64139844 VPS54 1.44374E−24 1 173490547 173490571 SLC9C2 1.46066E−24 1 185120927 185120940 TRMT1L 1.57643E−24 17 57937792 57937807 TUBD1 1.60716E−24 3 52696310 52696322 PBRM1 1.83711E−24 X 134025421 134025436 MOSPD1 2.09041E−24 2 157370018 157370033 GPD2 2.09277E−24 4 55976947 55976961 KDR  2.393E−24 18 40503735 40503751 RIT2 2.48943E−24 2 230656987 230657001 TRIP12  2.7448E−24 3 20189528 20189540 KAT2B 2.76665E−24 20 37191391 37191408 RALGAPB 3.21935E−24 7 138434066 138434081 ATP6V0A4 3.23489E−24 2 64806544 64806556 AFTPH 3.26179E−24 2 158275111 158275135 CYTIP 3.52321E−24 1 210411266 210411281 SERTAD4 3.58194E−24 2 86683539 86683575 KDM3A 3.72631E−24 1 42776699 42776711 FOXJ3 3.76862E−24 8 87751841 87751867 CNGB3 3.95052E−24 5 134086670 134086684 CAMLG(NM_001745: c.*30_*44del0) 4.26748E−24 8 101933023 101933037 YWHAZ 4.82347E−24 7 81695842 81695859 CACNA2D1 4.95872E−24 1 79383748 79383762 ELTD1 5.04093E−24 3 5249962 5249976 EDEM1 5.09083E−24 11 33374613 33374626 HIPK3 5.35266E−24 1 158584103 158584116 SPTA1 5.62348E−24 8 23712066 23712089 STC1(NM_003155: c.-30_-53del0) 5.72444E−24 5 14388797 14388816 TRIO 5.80373E−24 3 38257551 38257583 OXSR1  6.714E−24 18 29435778 29435795 TRAPPC8 6.89026E−24 1 54395673 54395692 HSPB11 6.93225E−24 5 50055456 50055473 PARP8 8.17131E−24 6 149846372 149846387 PPIL4 9.48992E−24 15 56946703 56946733 ZNF280D 1.11368E−23 20 48562797 48562813 RNF114 1.12626E−23 2 131883287 131883301 PLEKHB2  1.2191E−23 10 21461410 21461435 NEBL 1.31105E−23 13 73409508 73409522 PIBF1 1.34259E−23 15 43430749 43430765 TMEM62 1.35865E−23 6 15651642 15651656 DTNBP1 1.41445E−23 2 135887514 135887528 RAB3GAP1 1.44056E−23 14 21964623 21964635 TOX4 1.48711E−23 1 151384052 151384067 POGZ 1.49637E−23 12 10205420 10205435 CLEC9A 1.58202E−23 20 271204 271226 C20orf96 1.59463E−23 10 70056619 70056632 PBLD  1.623E−23 20 37146131 37146146 RALGAPB 1.67662E−23 13 48828102 48828118 ITM2B 1.68847E−23 10 27333121 27333134 ANKRD26 1.85758E−23 X 138864932 138864946 ATP11C  1.9878E−23 2 9558905 9558924 ITGB1BP1  2.0684E−23 2 101885656 101885675 CNOT11 2.15963E−23 9 130127691 130127703 GARNL3 2.16385E−23 8 59518439 59518456 NSMAF 2.19278E−23 6 145095545 145095558 UTRN 2.50911E−23 5 96342077 96342093 LNPEP 2.60313E−23 12 97306603 97306631 NEDD1 2.62054E−23 6 17675386 17675402 NUP153  2.824E−23 22 44083327 44083345 EFCAB6 2.89856E−23 5 10394911 10394930 MARCH6  3.025E−23 6 71571688 71571707 SMAP1(NM_001281439: c.*1751_*1770del0, 3.21041E−23 NM_021940: c.*1651_*1670del0, NM_001044305: c.*1651_*1670del0, NM_001281440: c.*1651_*1670del0) 3 113377481 113377493 KIAA2018 3.24595E−23 3 41877473 41877487 ULK4 3.47059E−23 14 60587879 60587900 PCNXL4 3.52279E−23 12 100496478 100496498 UHRF1BP1L 3.56689E−23 8 80831393 80831407 MRPS28 3.57504E−23 12 125587478 125587491 AACS 3.90401E−23 X 131233588 131233600 FRMD7 4.16916E−23 10 103567665 103567680 MGEA5 4.21675E−23 12 21639528 21639542 RECQL 4.37998E−23 9 131715001 131715017 NUP188 4.43058E−23 5 76785406 76785444 WDR41 4.83785E−23 X 23693084 23693098 PRDX4 4.90381E−23 3 33893929 33893949 PDCD6IP 5.05744E−23 1 89449508 89449520 RBMXL1 5.68388E−23 2 61566824 61566839 USP34 5.82621E−23 10 88834244 88834265 GLUD1 5.94791E−23 2 219341717 219341730 USP37 5.98493E−23 16 5129689 5129703 ALG1 6.07055E−23 19 14857187 14857203 EMR2 6.33804E−23 7 95775848 95775863 SLC25A13  6.5168E−23 1 46739974 46739989 RAD54L 6.88557E−23 10 74653468 74653479 OIT3(NM_152635: c.-89_-78del-) 6.96623E−23 3 48491343 48491366 ATRIP 6.97912E−23 20 8665502 8665518 PLCB1 7.52397E−23 6 30573637 30573656 PPP1R10 7.53381E−23 16 9010826 9010844 USP7 7.59901E−23 7 102727051 102727067 ARMC10 8.04084E−23 9 103027226 103027243 INVS  8.9062E−23 X 48156078 48156097 SSX1(dist = 29199), SSX9(dist = 4888) 9.26142E−23 12 28412398 28412416 CCDC91 9.31126E−23 14 31191658 31191682 SCFD1 9.73138E−23 9 97555228 97555242 C9orf3  9.8621E−23 7 6064470 6064488 EIF2AK1  1.0058E−22 1 10357206 10357224 KIF1B 1.03062E−22 8 38940143 38940157 ADAM9 1.05909E−22 8 97296205 97296220 PTDSS1  1.1449E−22 6 17669262 17669277 NUP153 1.16335E−22 1 176050430 176050447 RFWD2 1.30874E−22 12 50152601 50152618 TMBIM6  1.3139E−22 9 19078116 19078132 HAUS6 1.38134E−22 5 70837260 70837275 BDP1 1.64155E−22 8 96260054 96260070 C8orf37 1.66262E−22 8 86180906 86180924 CA13 1.72829E−22 8 28707622 28707636 INTS9 1.75063E−22 1 155686739 155686757 DAP3 1.86544E−22 19 6026288 6026302 RFX2 1.90685E−22 20 34435246 34435270 PHF20 2.02382E−22 14 91372685 91372700 RPS6KA5  2.2959E−22 3 93754286 93754317 ARL13B 2.37681E−22 1 172577864 172577879 SUCO 2.46375E−22 6 42626564 42626585 UBR2 2.59638E−22 8 62550924 62550938 ASPH 2.76163E−22 5 150846858 150846882 SLC36A1 2.76634E−22 6 84649715 84649747 CYB5R4 2.77451E−22 2 99721804 99721820 TSGA10 2.99882E−22 12 105538270 105538287 KIAA1033 3.07075E−22 4 76528928 76528945 CDKL2 3.13103E−22 1 214825289 214825312 CENPF 3.15603E−22 8 33356825 33356839 MAK16(NM_032509: c.*678_*692del0) 3.18837E−22 3 150282051 150282075 EIF2A 3.20711E−22 15 34380216 34380230 EMC7 3.20711E−22 6 46636556 46636581 SLC25A27 3.26649E−22 1 247729206 247729223 GCSAML 3.32916E−22 X 107918007 107918043 COL4A5 3.52105E−22 22 41551231 41551249 EP300  3.736E−22 1 202990110 202990128 TMEM183A, TMEM183B 3.84037E−22 7 5239305 5239336 WIPI2 3.87028E−22 2 102785158 102785171 IL1R1 4.12245E−22 14 55629650 55629664 DLGAP5 4.17582E−22 3 122471407 122471434 HSPBAP1 4.31879E−22 12 107237602 107237626 RIC8B  4.3971E−22 6 7413094 7413107 RIOK1 4.65995E−22 1 93691855 93691881 CCDC18 4.70356E−22 22 46679850 46679864 TTC38  4.7248E−22 4 113568126 113568140 LARP7 4.85516E−22 9 91083260 91083278 SPIN1 4.93324E−22 16 24574691 24574710 RBBP6  5.7931E−22 13 77792099 77792113 MYCBP2 5.87631E−22 2 8822892 8822918 ID2 6.24993E−22 13 77644856 77644877 MYCBP2 6.40289E−22 3 42660489 42660508 LOC101928323 6.54694E−22 5 137282031 137282059 FAM13B 6.61715E−22 19 36145409 36145425 COX6B1 7.51746E−22 1 74901739 74901760 FPGT-TNNI3K, TNNI3K 7.52798E−22 17 44409890 44409927 LRRC37A 7.54899E−22 13 43491778 43491796 EPSTI1  7.6162E−22 3 158526942 158526966 MFSD1 7.78369E−22 8 38839302 38839316 HTRA4 8.40849E−22 9 37887570 37887587 SLC25A51 8.53361E−22 7 152144203 152144216 FABP5P3(dist = 4103), LINC01003(dist = 16993) 8.74701E−22 16 71808499 71808519 AP1G1 8.85343E−22 4 9710633 9710651 MIR548I2(dist = 152696), DRD5(dist = 72607)  9.2485E−22 17 29195444 29195460 ATAD5 9.29572E−22 12 53861636 53861650 PCBP2 9.30239E−22 1 231094050 231094067 TTC13  9.4254E−22 17 39033672 39033684 KRT20 9.49511E−22 5 151180439 151180475 G3BP1 9.53371E−22 19 37721404 37721419 ZNF383   9.63E−22 7 7572355 7572381 COL28A1 9.95204E−22 12 104077096 104077126 STAB2 1.06863E−21 8 131193153 131193166 ASAP1  1.0715E−21 6 90503754 90503779 MDN1 1.07569E−21 2 211521213 211521243 CPS1 1.12102E−21 15 50782416 50782446 USP8 1.13234E−21 12 57006059 57006072 BAZ2A 1.29023E−21 9 86354663 86354679 GKAP1 1.29873E−21 10 17279211 17279223 VIM 1.31339E−21 13 115011550 115011564 CDC16 1.33337E−21 15 81187286 81187297 CEMIP 1.34615E−21 14 36334905 36334921 BRMS1L 1.36334E−21 X 24745018 24745047 POLA1 1.42309E−21 3 195022926 195022944 ACAP2  1.4349E−21 2 172187261 172187296 METTL8   1.46E−21 4 17841869 17841881 NCAPG 1.60179E−21 1 168165767 168165781 TIPRL 1.63795E−21 4 1701673 1701686 SLBP 1.63997E−21 2 152359276 152359297 NEB 1.70334E−21 X 23724675 23724698 ACOT9  1.7347E−21 13 50586051 50586064 DLEU2 1.73805E−21 15 52239617 52239629 LEO1 1.81414E−21 12 110454085 110454114 ANKRD13A 1.82095E−21 6 38905667 38905680 LOC100131047 1.87314E−21 6 36569717 36569737 SRSF3 1.96053E−21 10 89720622 89720649 PTEN 1.98143E−21 8 96047806 96047820 NDUFAF6 1.99857E−21 13 25073399 25073415 PARP4   2.01E−21 10 32575773 32575785 EPC1 2.07141E−21 14 102550069 102550088 HSP90AA1 2.09435E−21 16 21396850 21396873 SNX29P1 2.10082E−21 22 38766061 38766082 LOC400927 2.22577E−21 1 86435957 86435971 COL24A1 2.31018E−21 11 5687320 5687338 TRIM5  2.3563E−21 22 39079920 39079936 TOMM22(NM_020243: c.*74_*90del0) 2.44863E−21 4 141448595 141448610 ELMOD2 2.45085E−21 1 175116046 175116071 TNN 2.50258E−21 15 59806473 59806486 FAM81A 2.71323E−21 3 186522293 186522308 RFC4 2.71473E−21 1 245021291 245021305 HNRNPU 2.83883E−21 X 52674318 52674335 SSX7 2.90848E−21 1 78432506 78432521 FUBP1 2.98254E−21 21 35094849 35094878 ITSN1 2.99288E−21 8 63948170 63948202 GGH 3.24232E−21 1 93584864 93584885 MTF2 3.29637E−21 3 10103903 10103946 FANCD2 3.31269E−21 2 162081128 162081140 TANK 3.32769E−21 1 185269100 185269122 IVNSIABP 3.36381E−21 11 125763610 125763624 PUS3(NM_001271985: c.*70_*56del0, 3.45862E−21 NM_031307: c.*70_*56del0) 5 70818329 70818354 BDP1 3.46045E−21 15 52561891 52561907 MYO5C  3.6701E−21 17 74736999 74737016 MFSD11 3.70727E−21 13 52726707 52726730 NEK3 3.87017E−21 4 164440461 164440474 TMA16 3.97441E−21 X 19380975 19380993 MAP3K15 4.15548E−21 3 123332875 123332892 MYLK-AS1 4.19178E−21 14 104040415 104040450 APOPT1 4.40224E−21 15 48717850 48717884 FBN1 4.61042E−21 X 24084241 24084254 EIF2S3 5.86793E−21 19 1825786 1825805 REXO1 5.94048E−21 11 68338491 68338520 PPP6R3 6.43655E−21 9 79820192 79820224 VPS13A 6.44865E−21 21 34117067 34117080 PAXBP1  6.5632E−21 3 100438778 100438810 TFG 6.56367E−21 1 65138787 65138801 CACHD1 6.58731E−21 9 131456159 131456172 SET 6.67017E−21 1 10177680 10177693 UBE4B  6.7488E−21 11 18111872 18111889 SAAL1 7.01393E−21 5 78416973 78416990 BHMT 7.10922E−21 1 176105710 176105723 RFWD2 8.04665E−21 X 100793432 100793449 ARMCX4(dist = 42634), ARMCX1(dist = 12065) 8.31019E−21 6 20548795 20548808 CDKAL1 8.33373E−21 5 54710072 54710091 SKIV2L2 8.43081E−21 2 61145498 61145512 REL 8.68532E−21 12 45269439 45269452 NELL2(NM_001145109: c.103_98delins-) 9.40033E−21 2 98907089 98907103 VWA3B 9.97931E−21 3 37360696 37360708 GOLGA4 1.00925E−20 11 118883880 118883892 CCDC84 1.03126E−20 8 30464719 30464734 GTF2E2 1.05094E−20 2 64195997 64196012 VPS54 1.07643E−20 17 58289521 58289533 USP32 1.17896E−20 18 43445730 43445748 EPG5 1.20239E−20 14 20344373 20344394 OR4K2 1.21947E−20 4 146046123 146046135 ABCE1 1.23246E−20 2 139318332 139318366 SPOPL 1.35372E−20 4 141448696 141448718 ELMOD2  1.4123E−20 12 56504143 56504159 PA2G4 1.42391E−20 9 135773000 135773019 TSC1 1.54202E−20 X 129267464 129267478 AIFM1 1.54347E−20 3 37550027 37550040 ITGA9 1.62302E−20 6 17779922 17779935 KIF13A 1.69313E−20 14 52957731 52957750 TXNDC16 1.69585E−20 4 39233719 39233734 MIR1273H 1.73752E−20 8 68140383 68140394 ARFGEF1 1.75581E−20 15 30010328 30010349 TJP1 1.78485E−20 1 53267474 53267488 ZYG11B 1.85235E−20 1 109525421 109525434 WDR47 1.88444E−20 11 16339918 16339934 SOX6 1.91217E−20 3 160144007 160144039 SMC4 1.95037E−20 4 119666217 119666241 SEC24D  1.9873E−20 X 52654536 52654550 SSX8 2.03068E−20 3 30691871 30691882 TGFBR2 2.06284E−20 12 14599855 14599867 ATF7IP 2.20883E−20 13 31722620 31722638 HSPH1 2.25682E−20 2 135703650 135703664 CCNT2 2.31976E−20 15 51768755 51768768 DMXL2 2.36357E−20 10 21536939 21536956 NEBL-AS1(dist = 73087), CASC10(dist = 246465) 2.38852E−20 2 87122096 87122121 ANAPC1P1 2.39126E−20

TABLE 2 Microsatellite Repeat Marker Sequences for Esophageal Carcinoma (ESCA). TABLE 2 - ESCA ch start_pos end_pos ESCA (hg37) (hg37) (hg37) gene p-value 1 209974528 209974550 IRF6 0.000249688 1 245025697 245025717 HNRNPU 0.000301114 1 33087567 33087584 ZBTB8OS 0.000333 2 166758447 166758460 TTC21B 0.000333 1 184692999 184693020 EDEM3 0.000341763 7 102727051 102727067 ARMC10 0.000350877 3 132169705 132169718 DNAJC13 0.000370233 13 28133956 28133972 LNX2 0.000370233 3 129168854 129168881 IFT122 0.000370233 20 33033065 33033083 ITCH 0.000370233 14 31191658 31191682 SCFD1 0.000380518 20 58497481 58497497 SYCP2(NM_014258: c.-13_-29del0) 0.000380518 15 91303325 91303352 BLM(NM_001287248: c.-90_-63del-) 0.000380518 1 153617510 153617526 CHTOP 0.000391236 7 102825987 102826001 DPY19L2P2 0.000391236 4 146046123 146046135 ABCE1 0.000391236 10 33496676 33496688 NRP1 0.000391236 7 16722392 16722403 BZW2 0.000391236 10 101510104 101510123 CUTC 0.000402414 5 14678762 14678776 OTULIN 0.000402414 2 99614595 99614609 TSGA10(NM_025244: c.*65_*51del0, 0.000402414 NM_182911: c.*65_*51del0) 4 104066176 104066191 CENPE 0.000402414 9 131456159 131456172 SET 0.000414079 2 162081128 162081140 TANK 0.000414079 18 19119813 19119828 ESCO1 0.000414079 2 179548695 179548712 TTN 0.000414079 7 54819993 54820005 SEC61G(NM_014302: c.*111_*99del0, 0.000414079 NM_001012456: c*111_*99del0) 20 37191391 37191408 RALGAPB 0.000426257 4 146031236 146031253 ABCE1 0.000426257 13 79216356 79216381 RNF219 0.000426257 6 7413094 7413107 RIOK1 0.000426257 7 16676082 16676097 ANKMY2 0.000426257 9 86395372 86395398 GKAP1 0.000426257 6 53138203 53138233 ELOVL5 0.000426257 1 100542702 100542718 HIAT1 0.000426257 5 122940980 122941019 CSNKIG3 0.000438982 8 23712066 23712089 STC1(NM_003155: c.-30_-53del0) 0.000438982 12 89853387 89853405 POC1B 0.000438982 8 107704921 107704955 OXR1 0.000452284 12 45771901 45771918 ANO6 0.000452284 7 74608740 74608754 GTF2IP1, LOC100093631 0.000452284 5 33546113 33546143 ADAMTS12 0.000452284 5 74226391 74226403 FAM169A(dist = 63728), GCNT4(dist = 96886) 0.000452284 7 2406737 2406755 EIF3B 0.0004662 14 21964623 21964635 TOX4 0.0004662 2 120714401 120714418 PTPN4 0.0004662 6 111329221 111329239 RPF2 0.0004662 2 197531518 197531530 CCDC150 0.0004662 3 30691871 30691882 TGFBR2 0.0004662 3 67559216 67559229 SUCLG2 0.0004662 7 131113756 131113779 MKLN1 0.000480769 4 115586972 115586988 UGT8 0.000480769 5 118576096 118576110 DMXL1 0.000480769 1 185834851 185834865 HMCN1 0.000480769 17 35696841 35696853 ACACA 0.000480769 9 97555228 97555242 C9orf3 0.000496032 3 48491343 48491366 ATRIP 0.000496032 2 189926219 189926240 COL5A2 0.000496032 11 107518175 107518187 ELMOD1 0.000512033 10 74874082 74874112 NUDT13 0.000512033 15 52561891 52561907 MYO5C 0.000512033 12 88482779 88482791 CEP290 0.000512033 15 69714622 69714658 KIF23 0.000512033 20 37146131 37146146 RALGAPB 0.000528821 8 134125650 134125662 TG 0.000528821 12 25678995 25679008 LMNTD1 0.000528821 17 66033401 66033412 KPNA2 0.000546448 1 41456808 41456823 CTPS1 0.000546448 2 201778717 201778733 ORC2 0.000546448 11 118626215 118626227 DDX6 0.000546448 2 64112697 64112719 UGP2 0.000564972 2 37487341 37487353 PRKD3 0.000564972 2 197654578 197654593 GTF3C3 0.000564972 17 39522910 39522922 KRT33B 0.000564972 1 144918011 144918022 NBPF20, NBPF9, PDE4DIP 0.000564972 7 5087800 5087822 RBAK, RBAK-RBAKDN 0.000584454 4 169612452 169612484 PALLD 0.000604961 12 109510086 109510099 USP30 0.000604961 9 98703711 98703723 ERCC6L2 0.000604961 5 41909830 41909846 C5orf51 0.000626566 X 19037666 19037686 GPR64 0.000626566 3 150282051 150282075 EIF2A 0.000626566 12 124242458 124242472 ATP6V0A2 0.000649351 15 82517622 82517671 EFTUD1 0.000649351 10 71055448 71055460 HK1 0.000649351 5 14485161 14485175 TRIO 0.000649351 3 160144007 160144039 SMC4 0.000649351 14 53513439 53513452 DDHD1(NM_001160148: c.*47_*34del0, 0.000649351 NM_001160147: c.*47_*34del0, NM_030637: c.*47_*34del0) 2 15536509 15536532 NBAS 0.000649351 12 62972198 62972223 MON2 0.000673401 17 47076449 47076462 IGF2BP1 0.000673401 6 25452453 25452466 LRRC16A 0.000673401 19 51919434 51919447 LOC100129083, SIGLEC10 0.000673401 6 7595241 7595255 SNRNP48 0.000673401 1 9633387 9633400 SLC25A33 0.000673401 9 376186 376197 DOCK8 0.000673401 16 3350676 3350699 TIGD7(NM_033208: c.-62_-85del0) 0.000673401 12 8813345 8813362 MFAP5 0.000686342 2 47635523 47635537 MSH2 0.000698812 15 45725103 45725138 C15orf48 0.000698812 16 74372596 74372618 LOC283922 0.000698812 6 149846372 149846387 PPIL4 0.000698812 16 70176311 70176336 PDPR 0.000698812 8 17504626 17504637 MTUS1 0.000698812 2 39240584 39240596 SOS1 0.000725689 2 178364328 178364342 AGPS 0.000725689 3 107910327 107910342 IFT57 0.000725689 17 66141017 66141032 LINC00674(dist = 8947), LOC440461(dist = 53769) 0.000725689 3 180320897 180320910 TTC14 0.000754148 17 30293149 30293164 SUZ12 0.000754148 16 70595514 70595525 SF3B3 0.000754148 10 101992923 101992938 CWF19L1(NM_018294: c.*61_*46del0) 0.000754148 18 44424651 44424667 PLAS2 0.000754148 6 100006295 100006309 CCNC 0.000754148 2 66796098 66796109 MEIS1 0.000784314 15 65273147 65273161 SPG21 0.000784314 X 148582573 148582585 IDS 0.000784314 10 116196143 116196156 ABLIM1 0.000784314 11 58381663 58381676 ZFP91-CNTF 0.000784314 12 99060155 99060173 APAF1 0.000784314 16 68155860 68155874 NFATC3 0.000816327 1 237965133 237965146 RYR2 0.000816327 15 23333801 23333815 HERC2P2 0.000816327 7 26247984 26247997 CBX3 0.00085034 12 50867692 50867704 LARP 4 0.00085034 22 30772228 30772244 KIAA1656 0.000881575 7 98639904 98639917 SMURF1 0.000886525 7 152144203 152144216 FABP5P3(dist = 4103), LINC01003(dist = 16993) 0.000886525 1 221875661 221875686 DUSP10(NM_007207: c.*93_*68del0) 0.000886525 10 70669942 70669958 DDX50 0.000886525 3 135806702 135806713 PPP2R3A 0.000886525 12 95488339 95488354 FGD6 0.000903342 2 88875981 88875993 EIF2AK3 0.000925069 18 66367726 66367742 TMX3 0.000966184 3 132166148 132166162 DNAJC13 0.000966184 10 35314130 35314161 CUL2 0.00097371 8 67759411 67759438 C8orf44-SGK3, SGK3 0.001010101 14 76638065 76638087 GPATCH2L 0.001052632 5 78936847 78936860 PAPD4 0.001057082 12 21791410 21791426 LDHB 0.001057082 4 113178966 113178979 AP1AR 0.001057082 12 64491002 64491019 SRGAP1 0.001081081 16 67384060 67384075 LRRC36 0.00110742 14 56078699 56078713 KTN1 0.00110742 2 120620092 120620108 PTPN4 0.0011107 4 141448595 141448610 ELMOD2 0.001141553 17 20639183 20639199 LOC100287072 0.001141553 12 97306603 97306631 NEDD1 0.001207243 7 129680648 129680677 ZC3HC1 0.001207243 1 89289954 89289966 PKN2 0.001242236 12 69042454 69042468 RAP1B 0.001242236 11 86198529 86198542 ME3 0.001242236 1 212241691 212241730 DTL 0.001278772 2 61577667 61577680 USP34 0.001316945 8 65528842 65528854 CYP7B1 0.001316945 9 34017005 34017043 UBAP2 0.001316945 X 96171416 96171435 DIAPH2 0.001316945 18 12680595 12680617 CEP76, PSMG2 0.001316945 1 1920434 1920449 CFAP74 0.001316945 14 101506158 101506169 MIR376A1, MIR376A2, MIR376B, MIR654; MIR376C 0.001349528 12 122017848 122017866 KDM2B 0.001356852 12 51752085 51752103 GALNT6 0.001356852 2 70066571 70066582 GMCL1 0.001356852 19 9361740 9361752 OR7E24 0.001398601 13 25355954 25355978 RNF17 0.001422475 3 143235916 143235929 SLC9A9 0.001422475 6 20548795 20548808 CDKAL1 0.001442308 X 48214185 48214200 SSX3 0.001442308 7 102912317 102912336 DPY19L2P2 0.001442308 1 155583131 155583149 MSTO2P 0.001442308 11 87013273 87013284 TMEM135 0.001442308 6 102124470 102124483 GRIK2 0.001488095 5 137451361 137451372 NME5 0.001501502 3 20189528 20189540 KAT2B 0.001536098 3 113377481 113377493 KIAA2018 0.001586462 15 59094494 59094508 FAM63B 0.001587302 2 167138320 167138331 SCN9A 0.001639344 2 191155233 191155245 HIBCH 0.001680672 6 36452603 36452620 KCTD20 0.001680672 8 124382376 124382403 ATAD2 0.001680672 2 64806544 64806556 AFTPH 0.001680672 1 63270823 63270838 ATG4C 0.001694915 3 160395089 160395102 ARL14(NM_025047: c.-46_-33del-) 0.001694915 1 53267474 53267488 ZYG11B 0.001753361 X 2343183 2343213 DHRSX 0.00176315 1 113657018 113657033 LRIG2 0.001782531 12 48360947 48360961 TMEM106C 0.001814882 1 150676674 150676692 HORMAD1 0.001814882 14 32142544 32142557 NUBPL 0.001814882 13 25911034 25911067 NUPL1 0.001879699 12 104714847 104714867 TXNRD1 0.001948052 18 180211 180228 USP14 0.001948052 8 100160282 100160300 VPS13B 0.001948052 X 79991590 79991604 BRWD3 0.001948052 1 182812410 182812425 DHX9 0.001948052 1 211545442 211545459 TRAF5 0.001998002 9 75420448 75420463 TMC1 0.002020202 3 33626219 33626236 CLASP2 0.002020202 1 114963973 114963986 TRIM33 0.002020202 7 95775848 95775863 SLC25A13 0.002096436 2 27463091 27463105 CAD 0.002096436 10 95549836 95549852 LGI1 0.002105263 2 196762491 196762509 DNAH7 0.002162162 9 131715001 131715017 NUP188 0.002177068 17 57278908 57278920 PRR11 0.002221399 7 130139660 130139674 MEST 0.002262443 3 100569452 100569464 ABI3BP 0.002298851 2 11913727 11913739 LPIN1 0.002298851 11 88068256 88068270 CTSC 0.002352941 10 112211000 112211025 SMNDC1(dist = 146293), DUSP5(dist = 46600) 0.00244898 8 101933023 101933037 YWHAZ 0.002463054 5 59901692 59901704 DEPDC1B 0.002463054 4 88986745 88986761 PKD2 0.002463054 3 179298584 179298597 ACTL6A 0.002484472 8 96069973 96069988 NDUFAF6 0.00255102 17 40850552 40850587 CNTNAP1 0.00255102 9 80343587 80343612 GNAQ 0.002557545 1 217784431 217784441 GPATCH2 0.002645503 X 70594925 70594942 BCYRN1 0.002645503 1 86435957 86435971 COL24A1 0.002659574 11 71548312 71548339 DEFB108B 0.002775208 15 101550861 101550877 LRRK1 0.002797203 2 236817336 236817351 AGAP1 0.002884615 1 95615737 95615761 TMEM56, TMEM56-RWDD3 0.003030303 2 120366057 120366070 CFAP221 0.003030303 9 19334957 19334970 DENND4C 0.003278689 6 80910611 80910635 BCKDHB 0.003322259 6 32166160 32166174 NOTCH4 0.003389831 9 133498229 133498245 FUBP3 0.003417635 1 173797451 173797462 DARS2 0.003484321 15 80460576 80460591 FAH 0.003506721 3 196215451 196215463 RNF168 0.003658537 6 20758808 20758822 CDKAL1 0.003759398 4 119674051 119674062 SEC24D 0.003759398 1 158326447 158326459 CD1E 0.003759398 3 122471407 122471434 HSPBAP1 0.003805175 9 163927 163943 CBWD1 0.003846154 5 33561022 33561043 ADAMTS12 0.004040404 17 44409890 44409927 LRRC37A 0.004048583 4 15839700 15839712 CD38 0.004140787 5 96116095 96116125 ERAP1 0.004192872 15 63571279 63571293 APH1B 0.004192872 6 24589046 24589057 KIAA0319 0.004267425 5 70809269 70809285 BDP1 0.004354136 15 51017381 51017393 SPPL2A 0.004354136 6 152728079 152728093 SYNE1 0.004354136 17 65074354 65074364 HELZ(NM_014877: c.*14_*4del0) 0.004761905 19 22836873 22836886 ZNF492 0.004807692 14 64443258 64443278 MIR548AZ 0.005288207 7 117867960 117867983 ANKRD7 0.005288207 3 185155430 185155442 MAP3K13 0.005347594 11 125763610 125763624 PUS3(NM_001271985: c.*70_*56del0, 0.005347594 NM_031307: c.*70_*56del0) 22 16404838 16404857 POTEH(dist = 116901), OR11H1(dist = 43967) 0.005745554 6 152740681 152740695 SYNE1 0.005844535 8 17100456 17100471 CNOT7 0.006049607 4 38930985 38930995 FAM114A1 0.006060606 19 22585521 22585535 ZNF98 0.006265664 12 53861636 53861650 PCBP2 0.006342495 22 44083327 44083345 EFCAB6 0.006393862 X 79937622 79937634 BRWD3 0.006451613 2 43778857 43778869 THADA 0.006493506 5 14481270 14481282 TRIO 0.006535948 X 20204548 20204563 RPS6KA3 0.006535948 15 40005793 40005806 FSIP1 0.006584723 1 47325299 47325313 CYP4Z2P 0.006993007 6 70040500 70040513 BAI3 0.007211538 X 1464126 1464139 IL3RA 0.007389163 12 16713487 16713501 LMO3 0.008097166 6 133138067 133138082 RPS12 0.008534851 16 57249981 57250000 RSPRY1 0.008547009 14 96916232 96916246 AK7 0.009398496 17 18708830 18708843 TVP23B 0.009661836 7 23761159 23761171 STK31 0.01 2 7154826 7154836 RNF144A 0.01 2 230705516 230705530 TRIP12 0.01010101 13 33637913 33637928 KL 0.010989011 11 125488247 125488261 STT3A 0.010989011 8 131859768 131859803 ADCY8 0.011363636 16 90141288 90141302 PRDM7 0.011614402 13 115002097 115002111 CDC16 0.011904762 7 36465606 36465622 ANLN 0.012048193 6 15593319 15593334 DTNBP1 0.012048193 X 106092450 106092473 TBC1D8B 0.012195122 11 116629734 116629748 BUD13 0.012195122 10 102035182 102035193 BLOC1S2(NM_001282439: c.*37_*26del0, 0.012345679 NM_001282438: c.*37_*26del0, NM_001001342: c.*37_*26del0, NM_173809: c.*37_*26del0, NM_001282436: c.*37_*26del0, NM_001282437: c.*37_*26del0) 19 34951356 34951371 UBA2 0.0125 12 108104315 108104351 PWP1 0.0125 4 54265883 54265894 FIP1L1 0.0125 16 21623935 21623964 METTL9 0.012658228 6 126249747 126249771 NCOA7 0.012658228 1 112305406 112305423 DDX20 0.012658228 2 44934524 44934535 CAMKMT 0.012820513 15 76191743 76191755 UBE2Q2 0.012820513 7 149543201 149543232 ZNF862 0.012987013 17 1326754 1326769 CRK(NM_005206: c.*183_*168del0, 0.012987013 NM_016823: c.*53_*38del0) 15 41663884 41663900 NUSAP1 0.012987013 1 64022708 64022725 EFCAB7 0.013157895 20 34430474 34430486 PHF20 0.013333333 1 114186351 114186362 MAGI3 0.013333333 1 39929162 39929178 MACF1 0.013333333 2 271204 271226 C20orf96 0.013333333 1 210536178 210536190 HHAT 0.013333333 3 93754080 93754099 ARL13B 0.013333333 2 111406968 111406984 BUB1 0.013513514 11 16117460 16117478 SOX6 0.013513514 1 173490547 173490571 SLC9C2 0.013513514 3 125179711 125179723 SNX4 0.013513514 20 2552802 2552817 TMC2 0.013513514 19 35758789 35758801 LSR(NM_015925: c.*27_*39del0, 0.01369863 NM_205835: c.*27_*39del0, NM_205834: c.*27_*39del0, NM_001260490: c.*27_*39del0, NM_001260489: c.*27_*39del0) 12 97339669 97339680 NEDD1 0.01369863 7 131130509 131130538 MKLN1 0.01369863 1 100684334 100684355 DBT 0.01369863 1 20441896 20441907 PLA2G2D 0.01369863 14 68582259 68582279 RAD51B 0.013888889 6 117725383 117725399 ROS1 0.013888889 3 142402827 142402838 PLS1 0.013888889 8 22053163 22053178 BMP1 0.013888889 7 155099925 155099936 INSIG1 0.013888889 6 18258299 18258311 DEK 0.014084507 1 155701055 155701071 DAP3 0.014084507 15 81427705 81427719 C15orf26 0.014084507 20 13140617 13140637 SPTLC3 0.014084507 3 160131236 160131250 SMC4 0.014084507 2 204156968 204156980 CYP20A1 0.014084507 10 104449572 104449619 ARL3 0.014084507 4 151683003 151683021 LRBA 0.014084507 6 146256315 146256344 SHPRH 0.014285714 22 46679850 46679864 TTC38 0.014285714 5 37051861 37051873 NIPBL 0.014285714 2 192228419 192228444 MYO1B 0.014285714 5 14607339 14607351 FAM105A 0.014285714 4 25777985 25777996 SEL1L3 0.014285714 9 99408079 99408094 AAED1 0.014492754 1 149900985 149901002 MTMR11(NM_001145862: c.*36_*19del0) 0.014492754 3 52696310 52696322 PBRM1 0.014492754 10 90362299 90362324 LIPJ 0.014492754 7 5239305 5239336 WIPI2 0.014492754 2 236877066 236877084 AGAP1 0.014492754 6 108214754 108214783 SEC63 0.014492754 10 74899343 74899356 ECD 0.014705882 8 53543090 53543106 RB1CC1 0.014705882 17 30320860 30320882 SUZ12 0.014705882 14 74426284 74426298 COQ6 0.014705882 1 220284112 220284124 RNU5F-1 0.014705882 12 56380950 56380964 RAB5B 0.014705882 5 137451460 137451472 NME5 0.014705882 17 33288433 33288445 CCT6B(NM_001193530: c.-21_-33del0, 0.014705882 NM_001193529: c.-21_-33del0, NM_006584: c.-21_-33del0) 4 15826415 15826426 CD38 0.014705882 20 29449706 29449717 NONE(dist = NONE), FRG1B(dist = 162162) 0.014705882 6 160237662 160237680 PNLDCI 0.014705882 12 101598350 101598362 SLC5A8 0.014925373 3 186522293 186522308 RFC4 0.014925373 1 237060945 237060970 MTR(NM_000254: c.*1_*26del0, 0.014925373 NM_001291939: c.*1_*26del0, NM_001291940: c.*1_*26del0) 4 79754716 79754728 BMP2K 0.014925373 13 98634737 98634749 IPO5 0.014925373 10 64022582 64022593 RTKN2 0.014925373 14 21702046 21702071 HNRNPC 0.014925373 9 33886999 33887011 UBE2R2 0.014925373 15 59961570 59961607 BNIP2 0.014925373 2 158275111 158275135 CYTIP 0.014925373 11 108141955 108141971 ATM 0.014925373 20 58587783 58587794 CDH26 0.014925373 16 21559162 21559174 SLC7A5P2(dist = 27397), LOC101927814(dist = 41845) 0.014925373 13 45781539 45781550 GTF2F2 0.014925373 4 77276593 77276604 CCDC158 0.014925373 6 15651642 15651656 DTNBP1 0.015151515 17 62855003 62855017 LRRC37A3 0.015151515 10 116203903 116203928 ABLIM1 0.015151515 9 135523692 135523704 DDX31 0.015151515 8 42295130 42295156 SLC20A2 0.015151515 4 145659167 145659178 HHIP(NM_022475: c.*58_*69del0) 0.015151515 7 120590802 120590830 ING3(NM_019071: c.-134_-121delins-, 0.015151515 NM_198267: c.-134_-121delins-) 2 191523855 191523879 NAB1 0.015151515 4 5630470 5630482 EVC2 0.015239478 19 327260 327277 MIER2 0.015384615 15 81187286 81187297 CEMIP 0.015384615 14 45716018 45716030 MIS18BP1 0.015384615 20 3565277 3565289 ATRN 0.015384615 12 94575201 94575219 PLXNC1 0.015384615 12 31435608 31435620 FAM60A(NM_001135811: c.*38_*26del0, 0.015384615 NM_001135812: c.*38_*26del0, NM_021238: c.*38_*26del0) 9 19299209 19299224 DENND4C 0.015384615 6 136429995 136430013 PDE7B 0.015384615 6 17669303 17669328 NUP153 0.015384615 7 81695842 81695859 CACNA2D1 0.015384615 13 26151184 26151196 ATP8A2 0.015384615 17 1265304 1265326 YWHAE 0.015384615 19 21350520 21350533 ZNF431 0.015384615 17 27816599 27816619 TAOK1 0.015384615 12 105260159 105260194 SLC41A2 0.015384615 8 38880851 38880862 ADAM9 0.015384615 16 9186735 9186764 C16orf72 0.015384615 5 77745712 77745752 SCAMP1 0.015625 4 128621144 128621158 INTU 0.015625 12 42835328 42835365 PPHLN1(NM_201439: c.*17_*54del0, 0.015625 NM_201440: c.*17_*54del0, NM_001143788: c.*17_*54del0, NM_001143789: c.*17_*54del0, NM_201515: c.*17_*54del0) 2 160092703 160092716 WDSUB1 0.015625 19 34302673 34302689 KCTD15 0.015625 2 24521686 24521697 ITSN2 0.015625 21 34655334 34655346 IL10RB 0.015625 21 37706065 37706077 MORC3 0.015625 5 153174310 153174322 GRIA1 0.015625 X 134033226 134033239 MOSPD1 0.015625 7 75155143 75155157 PMS2P3 0.015625 20 7976762 7976773 TMX4 0.015625 2 64335290 64335301 PELI1 0.015625 11 27412757 27412806 LGR4 0.015625 19 14827076 14827089 ZNF333 0.015625 21 40871690 40871717 SH3BGR 0.015625 14 39788501 39788513 CTAGE5 0.015625 9 132595849 132595861 C9orf78 0.015873016 3 67058329 67058357 KBTBD8 0.015873016 6 89638988 89639004 RNGTT 0.015873016 2 170062201 170062216 LRP2 0.015873016 17 39659874 39659890 KRT13 0.015873016 12 88926290 88926302 KITLG 0.015873016 5 150856066 150856091 SLC36A1 0.015873016 1 22033369 22033411 USP48 0.015873016 5 38958956 38958971 RICTOR 0.015873016 X 11793084 11793105 MSL3 0.015873016 15 58974349 58974361 ADAM10 0.015873016 15 64231569 64231591 DAPK2 0.015873016 8 121502680 121502691 MTBP 0.015873016 16 72050826 72050853 DHODH 0.015873016 17 75187248 75187259 SEC14L1I 0.015873016 9 33364821 33364833 NFX1(NM_147133: c.*13_*25del0) 0.015873016 1 35826959 35826972 ZMYM4 0.015873016 X 30726149 30726160 GK 0.015873016 10 88753099 88753110 AGAP11 0.015873016 2 234178624 234178640 ATG16L1 0.016129032 1 173795803 173795821 DARS2 0.016129032 3 33725814 33725828 CLASP2 0.016129032 6 128330423 128330435 PTPRK 0.016129032 8 33356825 33356839 MAK16(NM_032509: c.*678_*692del0) 0.016129032 2 32366959 32366971 SPAST 0.016129032 3 132363752 132363765 NPHP3-ACAD11 0.016129032 9 123886190 123886202 CNTRL 0.016129032 14 21876732 21876743 CHD8 0.016129032 2 39505509 39505528 MAP4K3 0.016129032 4 128996166 128996178 LARP1B 0.016129032 1 64017377 64017388 EFCAB7 0.016129032 22 45828137 45828148 RIBC2 0.016129032 2 37152389 37152408 STRN 0.016129032 14 92258905 92258916 TC2N 0.016393443 1 12398426 12398437 VPS13D 0.016393443 11 118885668 118885701 CCDC84 0.016393443 2 70463334 70463348 TIA1 0.016393443 4 8472785 8472805 TRMT44 0.016393443 11 67209167 67209194 CORO1B 0.016393443 2 45645684 45645695 SRBD1 0.016393443 15 57545438 57545449 TCF12 0.016393443 1 52912109 52912134 ZCCHC11 0.016393443 5 60170512 60170537 ERCC8 0.016393443 9 32986030 32986069 APTX 0.016393443 10 121675238 121675251 SEC23IP 0.016393443 5 130535204 130535217 LYRM7 0.016393443 11 117152291 117152314 RNF214 0.016666667 2 211521213 211521243 CPS1 0.016666667 17 59857599 59857611 BRIP1 0.016666667 19 47700438 47700453 SAE1 0.016666667 4 159618683 159618709 ETFDH 0.016666667 2 179325203 179325214 MIR548N 0.016666667 8 130874614 130874639 FAM49B 0.016666667 9 123922400 123922412 CNTRL 0.016666667 11 60182851 60182862 MS4A14 0.016666667 3 9102112 9102129 SRGAP3 0.016666667 11 17526254 17526267 USH1C 0.016666667 8 22138812 22138831 PIWIL2 0.016666667 14 72941317 72941328 RGS6 0.016666667 20 49354351 49354368 PARD6B 0.016666667 10 48980563 48980577 GLUD1P7 0.016666667 15 56736722 56736733 MNS1 0.016666667 12 66716618 66716630 HELB 0.016666667 2 179363909 179363925 MIR548N 0.016666667 15 59399501 59399518 CCNB2 0.016666667 19 1364472 1364496 MUM1 0.016666667 5 86659147 86659159 RASA1 0.016666667 4 95170783 95170794 SMARCAD1 0.016666667 5 71500888 71500899 MAP1B 0.016666667 17 30538050 30538061 RHOT1 0.016666667 16 66884343 66884355 CA7 0.016666667 8 68140383 68140394 ARFGEF1 0.016949153 3 121515940 121515953 IQCB1 0.016949153 10 34573008 34573020 PARD3 0.016949153 15 86278759 86278785 AKAP13 0.016949153 16 71718538 71718563 PHLPP2 0.016949153 15 101019693 101019705 CERS3 0.016949153 3 160138723 160138736 SMC4 0.016949153 2 61622374 61622387 USP34 0.016949153 3 4669375 4669386 ITPR1 0.016949153 4 89352469 89352487 HERC6 0.016949153 17 73515055 73515068 TSEN54 0.016949153 21 34117067 34117080 PAXBP1 0.016949153 3 108175734 108175745 MYH15 0.016949153 7 76883792 76883819 CCDC146 0.016949153 5 118500981 118501000 DMXL1 0.016949153 20 33338325 33338339 NCOA6 0.016949153 1 46739974 46739989 RAD54L 0.016949153 3 16636093 16636108 DAZL 0.016949153 6 123545159 123545186 TRDN 0.016949153 2 165971883 165971895 SCN3A 0.016949153 7 23347410 23347421 MALSU1 0.016949153 15 94841380 94841419 MCTP2 0.016949153 7 56052489 56052500 GBAS 0.016949153 16 15141966 15141977 NTAN1, PDXDC1 0.016949153

TABLE 3 Microsatellite Repeat Marker Sequences for Glioblastoma Multiforme (GBM). TABLE 3 - GBM ch start_pos end_pos (hg37) (hg37) (hg37) gene GBM p-value 20 37146131 37146146 RALGAPB 6.35006E−10 17 18785823 18785842 PRPSAP2 9.26872E−10 19 327260 327277 MIER2 1.05996E−09 14 95999676 95999689 SNHG10 2.51832E−09 12 48360947 48360961 TMEM106C 4.44836E−09 11 117152291 117152314 RNF214 6.01553E−09 12 110720351 110720363 ATP2A2 1.34407E−08 10 74899343 74899356 ECD 1.83372E−08 17 74729588 74729600 METTL23 2.66069E−08 14 51348281 51348299 ABHD12B 3.46368E−08 15 44057632 44057645 PDIA3 3.70668E−08 7 86522420 86522432 KIAA1324L 3.92669E−08 2 47635523 47635537 MSH2 4.73369E−08 12 104461711 104461723 HCFC2 5.95548E−08 10 76349020 76349033 ADK 1.01211E−07 16 58585178 58585191 CNOTI 1.03024E−07 1 215931901 215931935 USH2A  1.2498E−07 8 141293914 141293943 TRAPPC9 1.39278E−07 2 61308569 61308585 KIAA1841 2.13551E−07 15 83808031 83808046 HDGFRP3  2.6195E−07 13 31722620 31722638 HSPH1 2.81205E−07 4 113568126 113568140 LARP7 3.49196E−07 1 86435957 86435971 COL24A1 3.61688E−07 1 78432506 78432521 FUBP1 3.70987E−07 17 39871551 39871566 GAST 4.77824E−07 2 27708007 27708031 IFT172 5.77336E−07 9 98230924 98230947 LOC100507346 7.01064E−07 6 136710669 136710685 MAP7 7.40825E−07 8 90933269 90933296 OSGIN2 7.52016E−07 7 121699789 121699802 PTPRZ1 8.68727E−07 4 128812230 128812245 PLK4 9.60345E−07 1 220355521 220355533 RAB3GAP2 1.15674E−06 7 135099044 135099059 CNOT4  1.2157E−06 16 15133783 15133795 NTAN1, PDXDC1 1.30846E−06 12 8693215 8693257 CLEC4E 1.32055E−06 7 91714092 91714106 AKAP9 1.33108E−06 4 57897508 57897530 IGFBP7 1.40045E−06 5 77745712 77745752 SCAMP1 1.50091E−06 X 15607586 15607598 ACE2 1.55681E−06 2 211179765 211179777 MYL1 1.59051E−06 2 62063093 62063111 FAM161A 1.59119E−06 7 106888946 106888972 COG5 2.32965E−06 1 235938388 235938400 LYST 2.56714E−06 6 42611936 42611951 UBR2 2.59603E−06 4 52928352 52928371 SPATA18 2.62044E−06 1 201754396 201754428 IPO9-AS1, RNU6-79P 2.63645E−06 7 95775848 95775863 SLC25A13 2.79898E−06 6 56504477 56504489 RNU6-71P 2.83185E−06 4 128621144 128621158 INTU 3.40001E−06 12 102512024 102512037 NUP37  3.9454E−06 12 989800 989815 WNK1 4.05912E−06 12 3018675 3018690 TULP3 4.43747E−06 1 223156384 223156419 DISP1 4.63349E−06 3 5024415 5024435 BHLHE40 5.17572E−06 12 56213978 56213991 ORMDL2 5.49765E−06 7 66463195 66463206 TYW1 5.49765E−06 4 41015553 41015566 APBB2 5.71317E−06 20 31954819 31954834 CDK5RAP1  5.895E−06 10 105752705 105752727 SLK 7.91627E−06 9 19334957 19334970 DENND4C 7.94569E−06 19 46299146 46299180 RSPH6A 8.58205E−06 2 64112697 64112719 UGP2 9.31961E−06 21 42823193 42823206 MX1 9.91146E−06 12 57882764 57882777 MARS 1.16881E−05 8 107704921 107704955 OXR1 1.17173E−05 9 125655308 125655324 RC3H2 1.22888E−05 4 39233719 39233734 MIR1273H  1.3431E−05 5 67576330 67576346 PIK3R1 1.46604E−05 3 197702875 197702887 LMLN 1.48703E−05 4 108935768 108935822 HADH 1.49272E−05 21 37787572 37787585 CHAF1B 1.52013E−05 3 44399683 44399706 TCAIM 1.57816E−05 16 84121078 84121113 MBTPS1 1.63044E−05 1 172577864 172577879 SUCO 1.67014E−05 9 112225552 112225564 PTPN3 1.73801E−05 5 10405809 10405822 MARCH6 1.77786E−05 11 700526 700541 TMEM80 1.78668E−05 15 73418741 73418756 NEO1  1.9685E−05 22 35719378 35719394 TOM1  2.0203E−05 10 98325237 98325262 TM9SF3 2.32964E−05 9 100997485 100997498 TBC1D2 2.56891E−05 12 104995800 104995813 CHST11 2.68605E−05 3 180320897 180320910 TTC14 2.73657E−05 19 7995974 7996007 TIMM44  2.8612E−05 6 88853530 88853542 CNR1(NM_001160259: c.*45_*33del0, 2.87436E−05 NM_001160226: c.*45_*33del0, NM_001160258: c.*45_*33del0, NM_033181: c.*45_*33del0, NM_016083: c.*45_*33del0) 1 16248728 16248740 SPEN 3.07607E−05 16 56535193 56535208 BBS2  3.1448E−05 6 10926514 10926528 SYCP2L 3.29636E−05 8 68140383 68140394 ARFGEF1 3.40205E−05 17 16056594 16056626 NCOR1 4.15863E−05 16 50368677 50368692 BRD7 4.18375E−05 10 114154662 114154673 ACSL5 4.23827E−05 4 42592935 42592965 ATP8A1 4.35132E−05 17 53014442 53014457 TOM1L1 4.39359E−05 8 17882845 17882857 PCM1 4.46847E−05 7 115891736 115891750 TES 4.48083E−05 12 72067966 72067980 THAP2 4.51671E−05 9 98009613 98009626 FANCC 4.87757E−05 20 36431202 36431215 CTNNBL1 5.05109E−05 8 67969596 67969610 COPS5 5.42673E−05 14 103915242 103915254 MARK3 5.45559E−05 1 23636874 23636886 HNRNPR(NM_001102397: c.*73_*61del0, 5.45607E−05 NM_001102398: c.*73_*61del0, NM_001102399: c.*73_*61del0, NM_001297621: c.*73_*61del0, NM_005826: c.*73_*61del0, NM_001297622: c.*73_*61del0, NM_001297620: c.*73_*61del0) 7 2406737 2406755 EIF3B 5.85864E−05 16 75665791 75665803 KARS  5.8725E−05 6 31624922 31624937 APOM 6.44903E−05 15 45968237 45968250 SQRDL 6.59546E−05 9 102730697 102730712 STX17 6.83924E−05 4 94693160 94693173 GRID2 6.94493E−05 3 160249220 160249234 KPNA4 6.94493E−05 3 69111084 69111116 UBA3 7.08642E−05 11 16339918 16339934 SOX6 7.26811E−05 2 211521213 211521243 CPS1 7.35759E−05 6 100957763 100957779 ASCC3 7.74931E−05 15 32393486 32393502 CHRNA7 7.87517E−05 3 113376110 113376147 KIAA2018 7.96718E−05 10 122630877 122630889 MIR5694 7.98148E−05 11 49196555 49196567 FOLH1 8.00293E−05 X 18323348 18323361 SCML2 8.25982E−05 2 228159652 228159677 LOC654841 8.41236E−05 11 57094842 57094869 SSRP1 8.51209E−05 3 19959707 19959719 EFHB 8.74126E−05 X 109507669 109507681 AMMECR1  8.9845E−05 17 15517060 15517073 CDRT1 9.13109E−05 9 131743701 131743715 NUP188 9.38174E−05 8 103287850 103287864 UBR5 9.56814E−05 1 65138787 65138801 CACHD1 9.65764E−05 2 202494630 202494642 TMEM237 9.79643E−05 5 77745862 77745874 SCAMP1 9.93093E−05 10 102035182 102035193 BLOCIS2(NM_001282439: c.*37_*26del0, 0.000101906 NM_001282438: c.*37_*26del0, NM_001001342: c.*37_*26del0, NM_173809: c.*37_*26del0, NM_001282436: c.*37_*26del0, NM_001282437: c.*37_*26del0) 5 74011541 74011556 HEXB 0.000104264 9 86588185 86588199 HNRNPK 0.000107448 12 107398862 107398876 CRY1 0.000107969 16 74920075 74920089 WDR59 0.000112918 7 139097271 139097295 C7orf55-LUC7L2, LUC7L2 0.000116128 6 137325901 137325917 IL20RA 0.000116206 14 39597463 39597482 GEMIN2 0.000122455 4 184570723 184570735 RWDD4 0.000123392 9 17464479 17464491 CNTLN 0.000127857 1 53255587 53255601 ZYG11B 0.000131496 19 34872355 34872367 GPI 0.000134548 21 38498341 38498356 TTC3 0.000137592 9 33912102 33912114 UBE2R2 0.000137741 6 137193301 137193332 PEX7 0.000138002 7 151884279 151884292 KMT2C 0.000141755 4 48381682 48381704 SLAIN2 0.000147362 3 170715672 170715694 SLC2A2 0.00015519 2 203817257 203817270 CARF 0.000166879 1 167889145 167889160 MPC2 0.00017307 10 96108988 96109000 NOC3L 0.000173085 10 50686600 50686614 ERCC6 0.000174192 3 52727189 52727200 GNL3 0.000182448 11 76157922 76157934 C11orf30 0.000182549 4 83970297 83970312 COPS4 0.000186059 3 121515940 121515953 IQCB1 0.000189973 2 175246545 175246557 CIR1 0.000196227 4 128724672 128724734 HSPA4L 0.00019802 1 211280724 211280748 KCNH1 0.000199584 13 51522081 51522094 RNASEH2B 0.000200337 5 14481270 14481282 TRIO 0.000202029 17 5044640 5044653 USP6 0.000206143 6 152539326 152539345 SYNE1 0.00021198 8 134125650 134125662 TG 0.000229417 11 55035809 55035822 TRIM48 0.000229473 19 11565819 11565831 ELAVL3 0.000234907 11 118247264 118247277 UBE4A 0.000240341 1 206904644 206904665 MAPKAPK2 0.000243546 2 112854563 112854576 TMEM87B 0.000251362 12 62261077 62261088 FAM19A2 0.000256725 15 89533168 89533181 MFGE8(dist = 76505), ABHD2(dist = 98200) 0.00025686 X 1464126 1464139 IL3RA 0.000265236 13 37602245 37602257 SUPT20H 0.0002725 17 8417006 8417020 MYH10 0.000274591 X 129267464 129267478 AIFM1 0.000282137 2 228680153 228680168 CCL20 0.000299587 16 4559351 4559367 HMOX2 0.000308196 5 94842718 94842730 TTC37 0.000319434 7 130139660 130139674 MEST 0.00032029 1 153955601 153955614 RAB13 0.000322915 17 39976721 39976731 FKBP10 0.000335345 2 99721804 99721820 TSGA10 0.000336818 14 56104386 56104405 KTN1 0.000341763 5 122940980 122941019 CSNK1G3 0.000345412 10 34573008 34573020 PARD3 0.000358836 X 148048207 148048223 AFF2 0.00036314 14 92258905 92258916 TC2N 0.000370233 15 50920509 50920523 TRPM7 0.00038346 1 103471456 103471487 COL11A1 0.000391752 11 1944050 1944071 TNNT3 0.000391937 1 204234196 204234213 PLEKHA6 0.000398144 17 8166113 8166126 PFAS 0.000406449 5 132408905 132408918 HSPA4 0.000419566 6 154489255 154489267 IPCEF1, OPRM1 0.000435414 6 64419024 64419039 PHF3 0.000438237 12 107237602 107237626 RIC8B 0.00045684 17 2323953 2323979 METTL16 0.000460066 2 98872570 98872582 VWA3B 0.000476677 1 179271948 179271961 SOAT1 0.000480031 3 185155430 185155442 MAP3K13 0.000482959 6 167416662 167416676 FGFR1OP 0.000500417 9 86354663 86354679 GKAP1 0.000509295 12 105464316 105464342 ALDH1L2 0.000509684 4 146076632 146076644 OTUD4 0.000513526 10 127789605 127789616 ADAM12 0.000529606 6 144758647 144758660 UTRN 0.000529801 17 17039561 17039595 MPRIP 0.000531476 3 47129781 47129808 SETD2 0.000536913 2 232025952 232025967 PSMD1 0.000539084 7 31132235 31132249 ADCYAP1R1 0.000558102 X 135095655 135095677 SLC9A6 0.000564972 8 74890927 74890949 TMEM70 0.000564972 18 649879 649895 TYMSOS(NM_001012716: c.*120_*104del0) 0.000566472 11 46665805 46665827 ATG13 0.00056684 12 73012649 73012663 TRHDE 0.000581636 2 152236045 152236060 TNFAIP6 0.000582411 9 19328009 19328021 DENND4C 0.000584454 4 110433282 110433303 SEC24B 0.000590958 11 14316128 14316148 RRAS2 0.000607903 1 46650191 46650201 TSPAN1 0.000641849 X 24084241 24084254 EIF2S3 0.000656689 17 47696764 47696775 SPOP 0.000657895 15 35149313 35149327 AQR 0.00066335 4 39511530 39511543 MIR1273H 0.000702272 15 81187286 81187297 CEMIP 0.000710773 1 235826382 235826396 LYST 0.000730997 12 90005161 90005173 ATP2B1 0.000738712 11 108121410 108121426 ATM 0.000743496 5 56546749 56546777 GPBP1 0.000745956 6 31646746 31646758 LY6G5C 0.000746911 10 70056619 70056632 PBLD 0.000770337 12 21958998 21959011 ABCC9 0.000806257 17 7811876 7811889 CHD3 0.000807723 3 196532148 196532160 PAK2 0.000812898 15 55841195 55841209 PYGO1 0.00081389 1 213180434 213180459 ANGEL2 0.000837872 19 35758789 35758801 LSR(NM_015925: c.*27_*39del0, 0.000839024 NM_205835: c.*27_*39del0, NM_205834: c.*27_*39del0, NM_001260490: c.*27_*39del0, NM_001260489: c._*27_*39del0) 6 138628598 138628611 KIAA1244 0.000840336 10 7755088 7755101 ITIH2 0.000869187 20 54823684 54823699 MC3R 0.00087108 6 90347394 90347406 LYRM2 0.000881368 18 57684454 57684466 PMAIP1(dist = 112916), MC4R(dist = 354098) 0.000883002 X 11200070 11200086 ARHGAP6 0.000911521 X 129203198 129203214 ELF4 0.000912545 6 160157277 160157288 WTAP 0.000948509 17 60374173 60374189 TBC1D3P2(dist = 21157), EFCAB3(dist = 73390) 0.001000834 21 43770926 43770938 TFF2 0.001010001 12 62785259 62785270 USP15 0.001012146 1 89289954 89289966 PKN2 0.001038422 19 33579248 33579262 GPATCH1 0.001042644 6 111702448 111702460 REV3L 0.001045033 6 76728583 76728598 IMPG1 0.001045033 1 20749284 20749296 THUMPD1 0.001076625 17 73519258 73519269 TSEN54 0.001085541 6 131999103 131999115 ENPP3 0.001101425 15 56946703 56946733 ZNF280D 0.001120239 21 33312539 33312554 HUNK 0.001122209 12 69214081 69214094 MDM2 0.00112225 3 127820493 127820505 RUVBL1 0.001134301 5 176729736 176729749 RAB24 0.001160656 2 56611386 56611398 CCDC85A 0.00116898 6 20548795 20548808 CDKAL1 0.001179485 4 152065328 152065339 SH3D19 0.001185771 6 128385949 128385967 LOC101928140 0.001207243 21 30339205 30339217 LTN1 0.001212121 6 102124470 102124483 GRIK2 0.001212573 X 150573322 150573335 VMA21 0.001232724 18 43445730 43445748 EPG5 0.001240695 18 19110456 19110477 ESCO1 0.001244912 16 3433714 3433726 ZSCAN32 0.001307076 5 147475501 147475520 SPINK5 0.001318571 15 45028919 45028931 TRIM69 0.00132632 1 84956161 84956173 RPF1 0.001360421 12 69090573 69090587 NUP107 0.001376994 1 155671899 155671929 DAP3 0.001380474 1 150310549 150310566 PRPF3 0.001388981 4 25315637 25315653 ZCCHC4 0.001394783 15 50935484 50935496 TRPM7 0.001414874 2 131883287 131883301 PLEKHB2 0.0014171 6 131948816 131948831 MED23 0.001456876 13 76134860 76134871 UCHL3 0.001488095 16 30665449 30665465 PRR14 0.00151747 5 50122645 50122660 PARP8 0.001541624 8 75157416 75157442 JPH1 0.001552554 2 98866980 98866995 VWA3B 0.001610133 21 37706087 37706100 MORC3 0.001639344 6 86387036 86387048 SNORD50A 0.001683313 17 35979746 35979761 DDX52 0.001731836 11 78154810 78154823 NARS2 0.001734906 5 63803508 63803522 RGS7BP 0.001738051 11 94230106 94230131 ANKRD49 0.00174216 17 59857599 59857611 BRIP1 0.001759531 12 97339669 97339680 NEDD1 0.001761597 15 64717845 64717857 TRIP4 0.001763357 14 58690427 58690451 ACTR10 0.001780898 9 15458080 15458092 SNAPC3 0.001797187 1 36888302 36888316 OSCP1 0.001807693 2 186692859 186692872 FSIP2 0.001818182 1 67154730 67154748 SGIP1 0.001822564 12 124144572 124144584 GTF2H3 0.001831502 2 98907089 98907103 VWA3B 0.001831502 1 233295992 233296007 PCNXL2 0.001845472 12 31820564 31820578 METTL20 0.001845472 2 20526998 20527011 PUM2 0.001851852 X 122598635 122598648 GRIA3 0.001854305 4 169612452 169612484 PALLD 0.001854305 12 124242458 124242472 ATP6V0A2 0.001858494 12 122966016 122966028 ZCCHC8 0.001867959 X 153357614 153357628 MECP2 0.001904589 10 75214137 75214149 PPP3CB 0.001905732 12 110924566 110924578 FAM216A 0.001923077 13 23808732 23808745 SGCG 0.001930502 15 78836661 78836676 PSMA4 0.001935484 13 39435552 39435564 FREM2 0.001950297 5 88018369 88018402 MEF2C(NM_001193350: c.*52_*19del0, 0.001980198 NM_001131005: c.*52_*19del0, NM_002397: c.*52_*19del0, NM_001193347: c.*52_*19del0, NM_001193348: c.*52_*19del0, NM_001193349: c.*52_*19del0) 12 53685372 53685383 ESPL1 0.002016129 14 88407716 88407730 GALC 0.002030991 X 15373247 15373259 PIR-FIGF 0.002059661 1 150297334 150297351 PRPF3 0.002060535 11 124007701 124007714 VWA5A 0.002087963 5 179665269 179665281 MAPK9 0.002094868 13 100913132 100913161 PCCA 0.002097693 5 68524006 68524019 MRPS36 0.002131035 1 181752769 181752784 CACNA1E 0.002134098 8 120856021 120856034 DSCC1 0.002136448 17 4646533 4646547 ZMYND15 0.002158342 3 52676065 52676079 PBRM1 0.002162162 2 139318332 139318366 SPOPL 0.002191132 14 58681903 58681915 ACTR10 0.002192982 14 45716018 45716030 MIS18BP1 0.002203442 5 6623405 6623418 NSUN2 0.002229122 5 76707435 76707447 PDE8B 0.002235584 4 107133861 107133873 TBCK 0.002237835 6 76618182 76618195 MY06 0.002243985 4 113107829 113107845 C4orf32 0.002248876 X 153714027 153714038 UBL4A 0.0022829 12 31289662 31289674 DDX11(dist = 31937), FAM60A(dist = 143846) 0.002337541 3 172046695 172046709 FNDC3B 0.002337541 4 16362275 16362287 TAPT1-AS1(dist = 102465), LDB2(dist = 140878) 0.002340183 11 5775903 5775915 OR52N4 0.002356638 11 94212930 94212942 MRE11A 0.002370417 16 53496428 53496451 RBL2 0.00238776 X 118679315 118679331 CXorf56 0.002392344 X 106028279 106028291 RNF128 0.002392344 16 31196218 31196237 FUS 0.002407981 6 17602786 17602812 FAM8A1 0.002414487 6 110048489 110048501 FIG4 0.002432596 7 23823176 23823194 STK31 0.002442002 12 30887772 30887832 CAPRIN2 0.002451559 11 65268479 65268492 MALAT1 0.002466236 13 114514907 114514927 TMEM255B 0.002466526 9 99408079 99408094 AAED1 0.002504472 19 8438454 8438467 ANGPTL4 0.002504472 3 113377481 113377493 KIAA2018 0.002505593 5 38954825 38954836 RICTOR 0.00255102 16 67286352 67286366 SLC9A5 0.002574003 2 39240584 39240596 SOS1 0.002579296 10 17646048 17646060 PTPLA 0.002583661 1 237619875 237619890 RYR2 0.002612179 5 137507104 137507121 BRD8 0.002617217 22 41550984 41550996 EP300 0.002621356 16 58200464 58200481 CSNK2A2 0.002645036 1 22837586 22837604 ZBTB40 0.002675318 6 121412191 121412203 TBC1D32 0.002681549 16 4835778 4835794 SEPT12 0.002721712 18 47438344 47438355 MYO5B 0.002747253 1 227218085 227218097 CDC42BPA 0.002757078 4 166388811 166388838 CPE 0.002757806 X 32472757 32472777 DMD 0.002758873 5 145888687 145888714 TCERG1 0.002830189 10 64975001 64975012 JMJD1C 0.002863632 1 196642969 196642979 CFH 0.002884615 X 153216185 153216195 HCFC1 0.002898551 19 47700438 47700453 SAE1 0.002919404 4 159618683 159618709 ETFDH 0.002919404 18 32917176 32917189 ZNF24(NM_006965: c.*20_*7del0) 0.002926233 17 62748076 62748093 LOC146880 0.002941372 2 48032740 48032754 MSH6 0.002943848 9 131456159 131456172 SET 0.002962023 3 113955055 113955069 ZNF80(NM_007136: c.*45_*31del0) 0.002965434 1 245021291 245021305 HNRNPU 0.00299578 3 3216976 3216988 CRBN 0.003005582 2 38527397 38527412 ATL2 0.003042156 5 130939025 130939037 RAPGEF6 0.003055768 13 101727043 101727094 NALCN 0.00305771 15 50570999 50571024 GABPB1 0.003072197 4 89772341 89772364 FAM13A 0.00308642 2 88484805 88484815 THNSL2 0.00310517 9 113530024 113530036 MUSK 0.003142184 12 9706558 9706571 DDX12P(dist = 105790), KLRB1(dist = 41299) 0.003164557 1 19683355 19683368 CAPZB 0.003193033 9 132595849 132595861 C9orf78 0.003260363 6 110426583 110426595 WASF1 0.003301246 17 36477914 36477929 MRPL45 0.003318584 8 24348425 24348437 LOC101929294, LOC101929315 0.003339296 1 12398426 12398437 VPS13D 0.003342246 18 12352952 12352964 AFG3L2 0.003378378 9 15433520 15433532 SNAPC3 0.003378378 2 120712718 120712731 PTPN4 0.003401039 10 96025381 96025392 PLCE1 0.003418803 3 138193025 138193038 ESYT3 0.003478027 X 108636043 108636070 GUCY2F 0.003496503 7 73666736 73666750 RFC2 0.003496503 6 55739711 55739726 BMP5(NM_021073: c.-48_-63del0) 0.003499563 2 66796098 66796109 MEIS1 0.003506311 5 180482303 180482317 BTNL9 0.003516352 2 102979238 102979250 IL18R1 0.003551745 6 110113763 110113776 FIG4 0.003596044 4 123109034 123109048 KIAA1109 0.003611449 12 88566358 88566370 TMTC3 0.003634476 4 119950975 119950989 SYNPO2 0.003653617 1 10468005 10468021 PGD 0.00367165 7 120739962 120739978 CPED1 0.003703051 11 63149670 63149682 SLC22A9 0.003753519 16 71808499 71808519 AP1G1 0.003773585 13 99461532 99461565 DOCK9 0.003805175 16 70693872 70693884 IL34 0.003834364 21 47662899 47662934 MCM3AP-AS1 0.003843748 8 7217010 7217023 ZNF705G 0.00385058 4 122590883 122590899 ANXA5 0.003851516 4 79460647 79460664 FRAS1 0.003856749 3 58792080 58792092 C3orf67 0.003864319 1 154227292 154227307 UBAP2L 0.003900525 14 31762500 31762511 HEATR5A 0.003912363 8 30569609 30569622 GSR 0.003923495 5 10397473 10397485 MARCH6 0.004048583 15 86278759 86278785 AKAP13 0.004058369 2 153004816 153004839 STAM2 0.004126142 2 79314062 79314073 REG1B 0.004158416 2 103281540 103281552 SLC9A2 0.004158416 5 139936680 139936694 SRA1 0.004162596 6 158322872 158322901 SNX9 0.004172571 12 72019989 72020018 ZFC3H1 0.004242424 15 65412325 65412337 PDCD7 0.004418843 8 17100456 17100471 CNOT7 0.004418843 3 179083024 179083036 MFN1 0.004450908 8 54742095 54742107 ATP6V1H 0.004508408 3 19498221 19498253 KCNH8 0.00452284 X 119675354 119675368 CUL4B 0.004559271 14 91633483 91633498 C14orf159 0.004586405 9 86584222 86584234 HNRNPK(NM_002140: c.*100_*88del0, 0.004605263 NM_031263: c.*100_*88del0, NM_031262: c.*43_*31del0) 19 16101139 16101166 OR10H4(dist = 40371), LINC00661(dist = 25278) 0.004617828 X 19024426 19024440 GPR64 0.004662005 X 48214185 48214200 SSX3 0.004667052 1 86246998 86247012 COL24A1 0.004734984 2 37487341 37487353 PRKD3 0.0049217 9 8525217 8525230 PTPRD 0.004980316 1 224318148 224318164 FBXO28 0.005078803 17 4712563 4712580 PLD2 0.005126452 14 50605267 50605280 SOS2 0.005202381 10 99118165 99118176 RRP12 0.005202381 1 113657018 113657033 LRIG2 0.005254919 7 129028857 129028882 AHCYL2 0.005254919 15 43307839 43307852 UBR1 0.005362615 11 89395303 89395315 FOLH1B 0.005580911 1 233225957 233225969 PCNXL2 0.005656566 11 107518175 107518187 ELMOD1 0.005689001 3 67058329 67058357 KBTBD8 0.005714286 1 215914883 215914896 USH2A 0.005745554 19 14153179 14153202 IL27RA 0.005806452 12 121004564 121004583 RNF10 0.00586178 1 150201305 150201316 ANP32E 0.005888848 14 73465027 73465043 ZFYVE1 0.005905042 5 70754289 70754302 BDP1 0.00593692 17 10543281 10543296 MYH3 0.005961252 4 54319247 54319262 FIP1L1 0.00599448 2 73635899 73635911 ALMS1 0.006036217 2 179478746 179478757 MIR548N, TTN-AS1 0.006171026 1 236902532 236902560 ACTN2 0.006240292 8 99054836 99054849 RPL30 0.00625077 14 53217376 53217395 STYX 0.006263261 12 55354876 55354889 TESPA1 0.006270479 19 11447769 11447783 RAB3D 0.006302521 13 41947712 41947725 NAA16 0.006341945 14 73079138 73079150 RGS6(dist = 45900), DPF3(dist = 6854) 0.006348087 8 104930646 104930658 RIMS2 0.00643897 1 9770690 9770741 PIK3CD 0.00647753 11 55656437 55656451 TRIM51 0.006588811 7 74172385 74172400 GTF2I 0.006593407 1 114224782 114224799 MAGI3 0.006672895 X 100793432 100793449 ARMCX4(dist = 42634), ARMCX1(dist = 12065) 0.006746627 15 58891938 58891962 ADAM10 0.006754862 12 99117397 99117414 APAF1 0.006820148 6 163235158 163235170 PACRG 0.00689138 4 48529683 48529699 FRYL 0.006896613 16 67470052 67470095 HSD11B2 0.006962785 5 68396764 68396793 SLC30A5 0.006993007 4 68416393 68416409 CENPC(dist = 5137), STAP1(dist = 8037) 0.007063882 2 207027356 207027368 EEF1 B2 0.007225164 4 123374811 123374832 IL2 0.007482453 17 31324395 31324414 SPACA3 0.007484766 4 120423686 120423697 PDE5A 0.007541478 1 15890342 15890359 DNAJC16 0.007545932 12 68690765 68690777 MDM1 0.007545932 2 271998 272015 ACP1 0.007548299 12 101598350 101598362 SLC5A8 0.007843137 6 42559866 42559879 UBR2 0.007928691 X 53113895 53113905 TSPYL2 0.0080453 15 42536227 42536238 TMEM87A 0.0080453 17 58289521 58289533 USP32 0.008064516 1 92846489 92846501 RPAP2 0.008130081 6 7410735 7410747 RIOK1 0.008130081

TABLE 4 Microsatellite Repeat Marker Sequences for is Lung Adenocarcinoma (LUAD). TABLE 4 - LUAD ch start_pos end_pos LUAD (hg37) (hg37) (hg37) gene p-value 15 101929632 101929652 PCSK6  2.5301E−08 12 107237602 107237626 RIC8B 3.53475E−06 20 37146131 37146146 RALGAPB 3.66148E−06 11 73984657 73984669 P4HA3 4.18157E−06 7 106888946 106888972 COG5 5.12958E−06 3 48636506 48636516 UQCRC1(NM_003365: c.*55_*45del0) 5.64524E−06 1 222904869 222904881 BROX 6.74941E−06 9 131456159 131456172 SET 7.61383E−06 12 63964640 63964653 DPY19L2 8.90139E−06 5 145647187 145647210 RBM27 9.24667E−06 5 68524006 68524019 MRPS36 1.05359E−05 14 23495610 23495622 PSMB5 1.11579E−05 12 49397291 49397302 PRKAG1 1.11957E−05 10 116919785 116919796 ATRNL1 1.32179E−05 7 121699789 121699802 PTPRZ1 2.46924E−05 1 218610662 218610680 TGFB2 2.55728E−05 10 26825151 26825168 APBB1IP 3.78529E−05 X 53113895 53113905 TSPYL2 3.84423E−05 2 231940295 231940307 PSMD1 4.64511E−05 8 104922508 104922534 RIMS2 4.86669E−05 2 99721804 99721820 TSGA10 5.43603E−05 6 24589046 24589057 KIAA0319 5.56948E−05 5 140812775 140812788 PCDHGA12 6.20732E−05 2 170062201 170062216 LRP2 6.30112E−05 1 82187543 82187554 LPHN2 7.21449E−05 4 71693494 71693508 GRSF1 7.25128E−05 X 129267464 129267478 AIFM1 7.67575E−05 12 73012649 73012663 TRHDE  9.1847E−05 6 55739711 55739726 BMP5(NM_021073: c.-48_-63del0) 0.000100547 14 96800846 96800858 ATG2B 0.000106372 11 14501267 14501282 COPB1 0.000108932 16 74372596 74372618 LOC283922 0.000112931 3 158526942 158526966 MFSD1 0.000116955 2 102979238 102979250 IL18R1 0.000120115 2 10269544 10269555 RRM2(NM_001165931: c.*31_*42del0, 0.000135483 NM_001034: c.*31_*42del0) 11 46703002 46703014 ARHGAP1 0.000140706 12 28459652 28459664 CCDC91 0.000143472 12 94575201 94575219 PLXNC1 0.000143472 1 211280724 211280748 KCNH1 0.000146282 22 31985385 31985398 SFI1 0.000149254 9 8525217 8525230 PTPRD 0.000151061 14 73079138 73079150 RGS6(dist = 45900), DPF3(dist = 6854) 0.000152277 1 92846489 92846501 RPAP2 0.000163613 15 20666397 20666411 HERC2P3 0.000165548 5 70837260 70837275 BDP1 0.000167701 1 11134470 11134485 EXOSC10 0.000216372 X 107464327 107464339 COL4A6 0.000216372 12 95488339 95488354 FGD6 0.000221484 17 57762402 57762414 CLTC 0.00022445 2 176995682 176995693 HOXD8 0.000235849 X 24084241 24084254 EIF2S3 0.000236183 X 48214185 48214200 SSX3 0.000246812 13 113965002 113965017 LAMP1 0.000251351 14 45587186 45587199 FKBP3 0.000251362 10 8111345 8111359 GATA3 0.000255363 5 77745712 77745752 SCAMP1 0.000256016 5 52358761 52358775 ITGA2 0.000268264 3 132173004 132173026 DNAJC13 0.000270819 12 8692327 8692338 CLEC4E 0.000273411 8 80831393 80831407 MRPS28 0.00027604 7 150918586 150918602 ABCF2 0.000281413 X 135481956 135481970 GPR112 0.00028342 21 42598164 42598175 BACE2 0.000284158 6 56504477 56504489 RNU6-71P 0.000287356 2 128263363 128263377 IWS1 0.00029264 9 86354663 86354679 GKAP1 0.000295479 2 27597190 27597204 SNX17 0.000299303 9 97555228 97555242 C9orf3 0.000302746 12 133237753 133237768 POLE 0.000306373 1 207753824 207753846 CR1 0.000307645 7 98639904 98639917 SMURF1 0.000308642 2 39240584 39240596 SOS1 0.000316196 8 101933023 101933037 YWHAZ 0.00031736 7 75185990 75186002 HIP1 0.000318725 9 127287158 127287183 NR6A1 0.000340101 10 25140413 25140425 PRTFDC1 0.000342924 3 180320897 180320910 TTC14 0.000345781 13 99890849 99890862 MIR548AN 0.000348675 2 119739127 119739142 MARCO 0.000349824 4 89352469 89352487 HERC6 0.000351605 18 649879 649895 TYMSOS(NM_001012716: c.*120_*104del0) 0.000357577 6 102337480 102337497 GRIK2 0.000357782 12 50867692 50867704 LARP4 0.000363372 11 128350396 128350418 ETS1 0.000364277 2 207013834 207013846 NDUFS1 0.000369987 5 10405809 10405822 MARCH6 0.000369987 4 39233719 39233734 MIR1273H 0.000372456 15 81427705 81427719 C15orf26 0.000383054 12 56213978 56213991 ORMDL2 0.000385208 1 167871297 167871312 ADCY10 0.00038961 8 24348425 24348437 LOC101929294, LOC101929315 0.000396825 14 96848565 96848580 GSKIP 0.00039984 14 21960425 21960451 TOX4 0.000442087 2 211179765 211179777 MYL1 0.000452515 5 68662287 68662298 AK6, TAF9 0.000454442 10 34573008 34573020 PARD3 0.000455982 1 165712555 165712571 TMCO1 0.000463177 1 113159364 113159384 ST7L 0.000469339 1 237060945 237060970 MTR(NM_000254: c.*1_*26del0, 0.000470544 NM_001291939: c.*1_*26del0, NM_001291940: c.*1_*26del0) 5 38954825 38954836 RICTOR 0.000471698 16 5129689 5129703 ALG1 0.000474169 8 134125650 134125662 TG 0.000474293 1 150799125 150799138 ARNT 0.000477669 19 36564438 36564455 WDR62 0.000477669 1 116655183 116655197 MAB21L3(NM_152367: c.-54_-40del-) 0.000479074 1 12330939 12330953 VPS13D 0.000482625 1 173795803 173795821 DARS2 0.000489115 2 61308569 61308585 KIAA1841 0.000489115 12 90005161 90005173 ATP2B1 0.000492587 11 124007701 124007714 VWA5A 0.000493197 6 110426583 110426595 WASF1 0.000500417 1 116940481 116940497 ATP1A1-AS1 0.000500581 5 118451836 118451847 DMXL1 0.000502513 15 50782416 50782446 USP8 0.00050478 16 4873743 4873761 GLYR1 0.000514282 20 36431202 36431215 CTNNBL1 0.000514386 17 73515055 73515068 TSEN54 0.000517974 11 119145463 119145476 CBL 0.000517974 15 64717845 64717857 TRIP4 0.000523013 3 132169705 132169718 DNAJC13 0.000532611 17 45105631 45105644 RPRML(dist = 49017), ARL17A(dist = 3308) 0.000551572 2 175246545 175246557 CIR1 0.000556567 17 39659874 39659890 KRT13 0.000560119 11 124624705 124624721 ESAM 0.000570633 14 35497274 35497286 SRP54 0.000574581 1 85575838 85575853 WDR63 0.000589251 21 34117067 34117080 PAXBP1 0.000603819 2 47635523 47635537 MSH2 0.000613834 6 25452453 25452466 LRRC16A 0.000639987 2 101581294 101581308 NPAS2 0.000652032 2 95783701 95783713 MRPS5 0.000662468 17 61958954 61958979 GH2 0.000678841 1 65138787 65138801 CACHD1 0.000684265 12 132496182 132496193 EP400 0.000686342 5 112903585 112903598 YTHDC2 0.000693963 9 73164596 73164610 TRPM3 0.000697569 3 172080401 172080412 FNDC3B 0.00071286 14 31191658 31191682 SCFD1 0.000716363 15 40951461 40951477 CASC5 0.000716675 19 36572251 36572263 WDR62 0.000750912 X 108636043 108636070 GUCY2F 0.000756305 1 241954005 241954024 WDR64 0.000761589 3 129155547 129155558 MBD4 0.000766088 11 65268479 65268492 MALAT1 0.000770331 6 96982111 96982125 UFL1 0.000783699 1 153955601 153955614 RAB13 0.000807275 11 117152291 117152314 RNF214 0.000812898 19 14104688 14104703 RFX1(NM_002918: c.-33_-48del0) 0.000844736 6 36452603 36452620 KCTD20 0.000844736 1 159166612 159166624 CADM3-AS1 0.000855178 12 109510086 109510099 USP30 0.000889522 11 16339918 16339934 SOX6 0.000889522 2 118854094 118854108 INSIG2(NM_016133: c.-39_-25del-) 0.000964295 7 73279233 73279260 WBSCR28 0.000964721 3 33725814 33725828 CLASP2 0.00098736 11 63149670 63149682 SLC22A9 0.000995419 1 50663196 50663209 ELAVL4 0.001003578 13 28133956 28133972 LNX2 0.001011837 19 9771286 9771300 ZNF562 0.001034752 6 163235158 163235170 PACRG 0.001037235 10 81036869 81036879 ZMIZ1 0.001042644 17 30320860 30320882 SUZ12 0.001081742 14 95999676 95999689 SNHG10 0.001084735 19 35758789 35758801 LSR(NM_015925: c.*27_*39del0, 0.001084735 NM_205835: c.*27_*39del0, NM_205834: c.*27_*39del0, NM_001260490: c.*27_*39del0, NM_001260489: c.*27_*39del0) 9 80343587 80343612 GNAQ 0.001090986 4 8472785 8472805 TRMT44 0.001096742 5 176729736 176729749 RAB24 0.001096987 9 86588185 86588199 HNRNPK 0.001149027 16 19481220 19481235 TMC5 0.001256808 2 120714401 120714418 PTPN4 0.001312605 11 134118382 134118401 THYN1 0.001385696 7 92129161 92129183 PEX1 0.001438858 5 67576330 67576346 PIK3R1 0.001438858 10 17110577 17110588 CUBN 0.001441708 15 52561891 52561907 MYO5C 0.001448641 12 31820564 31820578 METTL20 0.00149231 12 121004564 121004583 RNF10 0.001492773 6 157495951 157495966 ARID1B 0.001501185 X 100530312 100530326 TAF7L 0.001569607 17 39871551 39871566 GAST 0.001571151 6 111702448 111702460 REV3L 0.001574357 5 14485161 14485175 TRIO 0.001577546 11 71548312 71548339 DEFB108B 0.001585786 10 43199666 43199677 LINC01518(dist = 12459), BMS1(dist = 78277) 0.00160422 2 172314644 172314656 DCAF17 0.001624915 14 76524970 76524982 IFT43 0.001632604 5 179150788 179150800 CANX 0.001635852 13 113818805 113818818 PROZ 0.001661959 11 59368218 59368235 OSBP 0.001754454 1 99164246 99164260 SNX7 0.001763357 2 183960133 183960155 DUSP19 0.001796025 15 101019693 101019705 CERS3 0.001812178 11 118369265 118369290 KMT2A 0.001823505 4 101337123 101337134 EMCN 0.001842536 6 133093231 133093247 SLC18B1 0.00193585 2 173848186 173848214 RAPGEF4 0.001996891 17 74286032 74286047 QRICH2 0.002005228 19 11565819 11565831 ELAVL3 0.002018712 7 134626034 134626049 CALD1 0.002060535 1 112303077 112303090 DDX20 0.002062152 14 68582259 68582279 RAD51B 0.002093745 4 79754716 79754728 BMP2K 0.002144873 17 4646533 4646547 ZMYND15 0.002219289 2 206911191 206911211 INO80D 0.002253229 20 60963346 60963359 RPS21 0.002321725 9 52625 52641 FAM138C(dist = 16761), PGM5P3-AS1(dist = 20049) 0.002502187 7 95442405 95442420 DYNC1I1 0.002512967 15 55972660 55972674 PRTG 0.002598137 2 179616770 179616786 TTN 0.00268172 14 91639611 91639627 C14orf159 0.002742018 1 234565078 234565090 TARBP1 0.002836165 X 100793432 100793449 ARMCX4(dist = 42634), ARMCX1(dist = 12065) 0.002877698 2 21226218 21226230 APOB 0.003019997 7 81641570 81641584 LOC101927356 0.003075233 12 27841925 27841938 PPFIBP1 0.003110914 1 235621851 235621865 B3GALNT2 0.003236992 15 41770639 41770652 RTF1 0.00328121 15 40005793 40005806 FSIP1 0.003332107 11 55656437 55656451 TRIM51 0.003399405 6 43021976 43021989 MRPL2(NM_015950: c.*36_*23del0, 0.003422944 NM_001300848: c.*202_*189del0) 12 99117397 99117414 APAF1 0.003618497 6 136710669 136710685 MAP7 0.00367396 7 26883761 26883776 SKAP2 0.003678084 3 15613279 15613304 HACL1 0.003762378 6 20758808 20758822 CDKAL1 0.003922319 17 74721967 74721983 JMJD6 0.003984394 1 63044645 63044661 DOCK7 0.004034497 6 133138067 133138082 RPS12 0.004087252 13 33637913 33637928 KL 0.004100523 6 121412191 121412203 TBC1D32 0.004148696 5 134015250 134015288 SEC24A 0.004255319 1 109856836 109856854 SORT1 0.004274795 9 5811331 5811349 ERMP1 0.00456621 12 110720351 110720363 ATP2A2 0.004598134 12 53861636 53861650 PCBP2 0.00460591 14 64443258 64443278 MIR548AZ 0.004728293 8 75944409 75944422 CRISPLD1 0.004777562 2 238925144 238925166 UBE2F-SCLY 0.004830918 1 117911178 117911189 MAN1A2 0.004830918 22 44368728 44368741 SAMM50 0.004871187 X 100666907 100666921 HNRNPH2, RPL36A-HNRNPH2 0.004878049 3 42599049 42599064 SEC22C 0.004933759 5 54552380 54552391 DHX29 0.004950495 7 36465606 36465622 ANLN 0.005071541 1 115262366 115262389 CSDE1 0.005076142 2 10928694 10928709 PDIA6 0.005164222 9 96209987 96209999 FAM120AOS 0.005265236 20 6077429 6077449 FERMT1 0.005299223 13 78137932 78137946 SCEL 0.005541183 X 135630678 135630689 VGLL1 0.005552794 14 39594134 39594146 GEMIN2 0.005813953 7 84671609 84671620 SEMA3D 0.005813953 4 39511530 39511543 MIR1273H 0.005999859 12 48360947 48360961 TMEM106C 0.006000513 15 101550861 101550877 LRRK1 0.006104998 1 54692854 54692865 SSBP3 0.00617284 4 41015553 41015566 APBB2 0.006231221 6 126075709 126075734 HEY2 0.00627802 5 74722305 74722316 COL4A3BP 0.006289308 19 55438923 55438944 NLRP7 0.006369045 2 88484805 88484815 THNSL2 0.006410256 3 188242333 188242358 LPP 0.006410256 2 238419543 238419568 MLPH 0.006530381 4 39871117 39871154 PDS5A 0.006530381 2 54125185 54125196 PSME4 0.006622517 4 84519775 84519790 AGPAT9 0.006843973 5 131924346 131924374 RAD50 0.006896552 X 154456644 154456657 VBP1 0.006994412 14 51348281 51348299 ABHD12B 0.007009585 1 109617803 109617815 TAF13 0.007042254 12 113645152 113645163 IQCD 0.007142857 12 57032216 57032235 ATP5B 0.00729927 5 75858199 75858210 IQGAP2 0.007352941 20 46270911 46270923 NCOA3 0.007575758 17 30500816 30500828 RHOT1 0.007604563 1 179561673 179561709 TDRD5(NM_001199091: c.-78_-42del-) 0.007633588 17 74736999 74737016 MFSD11 0.007756119 1 91402917 91402929 ZNF644 0.007784946 7 107336262 107336274 SLC26A4 0.0078125 2 111881263 111881275 BCL2L11 0.0078125 10 93601945 93601955 TNKS2 0.007874016 17 62855003 62855017 LRRC37A3 0.008 X 154009644 154009656 MPP1 0.008130081 X 19606999 19607014 SH3KBP1 0.008333333 14 92549604 92549623 ATXN3 0.008583691 2 43768233 43768244 THADA 0.00862069 17 37657460 37657471 CDK12 0.008624591 4 15642515 15642535 FBXL5 0.008733624 2 189859434 189859447 COL3A1 0.00877193 4 146076632 146076644 OTUD4 0.00878035 X 110494528 110494543 CAPN6 0.008849558 13 73409508 73409522 PIBF1 0.008866553 10 12215870 12215884 NUDT5 0.00904258 8 68139326 68139338 ARFGEF1 0.009049774 8 124382376 124382403 ATAD2 0.009090909 19 34687462 34687485 LSM14A 0.009259259 17 67178976 67178992 ABCA10 0.009421209 4 38937316 38937329 FAM114A1 0.009478673 1 243736210 243736226 AKT3 0.009508655 17 2323953 2323979 METTL16 0.00952381 10 93841262 93841273 CPEB3 0.009661836 2 238271786 238271797 COL6A3 0.009674113 18 21293834 21293881 LAMA3 0.009708738 X 31200799 31200843 DMD 0.009860334 21 19653342 19653355 TMPRSS15 0.009896847 19 54400979 54401003 PRKCG 0.00990099 1 47123898 47123914 ATPAF1 0.009979494 16 15133783 15133795 NTAN1, PDXDC1 0.010032747 1 46726867 46726890 RAD54L 0.010050251 5 70797500 70797521 BDP1 0.01010101 11 46666872 46666883 ATG13 0.010152284 6 149718577 149718593 TAB2 0.010362694 6 18258299 18258311 DEK 0.010638298 12 120741303 120741326 SIRT4 0.010695187 11 132179950 132179979 NTM 0.010752688 X 35944077 35944088 CXorf22 0.010752688 12 26816832 26816843 ITPR2 0.010752688 11 104879686 104879697 CASP5 0.010810811 1 31766005 31766017 SNRNP40 0.010928962 8 38153186 38153199 WHSC1L1 0.010928962 2 167138320 167138331 SCN9A 0.010935187 11 86120270 86120294 CCDC81 0.011049724 7 8110836 8110848 GLCCI1 0.011049724 12 53470811 53470838 SPRYD3 0.011049724 17 16056594 16056626 NCOR1 0.011049724 5 131927539 131927561 RAD50 0.011111111 2 111397237 111397251 BUB1 0.011114006 15 51768755 51768768 DMXL2 0.011173184 18 14214318 14214331 ANKRD20A5P 0.011363636 15 66794298 66794311 RPL4 0.011363636 7 112555294 112555307 C7orf60 0.011406844 7 38282130 38282151 STARD3NL(dist = 11858), TARP(dist = 17093) 0.011433093 6 28876873 28876904 TRIM27 0.011450382 12 97051927 97051940 CDK17(dist = 257561), NEDD1(dist = 249061) 0.011466421 17 41256074 41256122 BRCA1 0.01146862 6 17292448 17292460 RBM24(NM_001143942: c.*98_*110del0, 0.011494253 NM_001143941: c.*98_*110del0, NM_153020: c.*98_*110del0) 1 154178185 154178198 C1orf189 0.011494253 3 62459813 62459846 CADPS 0.011494253 11 49088577 49088602 TRIM64C(dist = 7913), FOLH1(dist = 79585) 0.01150398 4 178357514 178357527 AGA 0.011560694 20 35660978 35660989 RBL1 0.011560694 2 58362150 58362161 VRK2 0.011764706 X 134025421 134025436 MOSPD1 0.011811024 11 55339545 55339556 OR4C16 0.011811024 11 74053485 74053497 PGM2L1 0.011857708 7 103828911 103828922 ORC5 0.011904762 15 52239617 52239629 LEO1 0.011952191 15 34434467 34434479 KATNBL1(NM_024713: c.*73_*61del0) 0.011988012 19 51919434 51919447 LOC100129083, SIGLEC10 0.012 17 8417006 8417020 MYH10 0.012021927 1 54252939 54252952 NDC1 0.012048193 4 83970297 83970312 COPS4 0.012048193 6 5000724 5000762 RPP40 0.012048193 1 220269426 220269439 RNU5F-1 0.012121212 6 130761525 130761543 TMEM200A 0.012145749 15 43990706 43990741 CKMT1A 0.012195122 21 38564530 38564545 TTC3 0.012195122 2 55863360 55863372 PNPT1 0.012200061 11 47187055 47187087 ARFGAP2 0.012244898 18 3597089 3597100 DLGAP1-AS1 0.012244898 2 238005446 238005457 COPS8 0.012269939 11 89395303 89395315 FOLH1B 0.012327142 X 48631645 48631660 GLOD5 0.012345679 10 52566432 52566445 A1CF(NM_001198820: c.*57_*44del0, 0.01242236 NM_014576: c.*57_*44del0, NM_138932: c.*57_*44del0, NM_001198819: c.*57_*44del0, NM_001198818: c.*57_*44del0, NM138933: c.*57_*44del0) 16 69385403 69385421 TMED6 0.012448133 7 91714092 91714106 AKAP9 0.012448133 2 187466921 187466932 ITGAV 0.0125 6 32155249 32155264 PBX2 0.0125 10 112044559 112044572 MXI1 0.012552301 12 7187777 7187796 C1R(NM_001733: c.*59_*40del0) 0.012552301 9 113449613 113449633 MUSK 0.012578616 5 137507104 137507121 BRD8 0.012586287 1 109349996 109350021 STXBP3 0.012658228 7 137076100 137076123 DGKI 0.012711864 11 4150238 4150253 RRM1 0.012738854 X 103164079 103164090 MIR1256 0.012738854 21 37425988 37425999 SETD4 0.012738854 10 102716310 102716330 FAM178A 0.012875536 20 34430474 34430486 PHF20 0.012987013 12 51323672 51323684 METTL7A 0.012987013 1 22837586 22837604 ZBTB40 0.013034757 2 152424933 152424962 NEB 0.013043478 7 5087800 5087822 RBAK, RBAK-RBAKDN 0.013043478 6 109480681 109480693 CEP57L1 0.013043478 18 12955439 12955452 SEH1L 0.01310075 7 100319680 100319696 EPO 0.013157895 1 16245610 16245621 SPEN 0.013157895 10 115380483 115380497 NRAP 0.013215859 X 18183097 18183113 BEND2(NM_153346: c.*32_*16del0) 0.013215859 22 21968716 21968730 UBE2L3 0.013215859 20 31294314 31294329 COMMD7 0.013245033 14 50760968 50760980 L2HGDH 0.013274336 1 158298679 158298691 CD1B 0.013274336 X 19086800 19086823 GPR64 0.013274336 10 12162338 12162351 DHTKD1 0.013333333 2 79314062 79314073 REG1B 0.013333333 1 200080464 200080490 NR5A2 0.013333333 2 98872570 98872582 VWA3B 0.013333333 7 73254451 73254472 WBSCR27 0.013333333 13 26967446 26967495 CDK8 0.013392857 1 46650191 46650201 TSPAN1 0.013413889 5 108673063 108673074 PJA2 0.013422819 3 10128965 10128985 FANCD2, FANCD2OS 0.013513514 5 72875091 72875102 UTP15 0.013513514 17 62532622 62532635 CEP95 0.013513514 1 197009613 197009644 F13B 0.013574661 1 211545442 211545459 TRAF5 0.013590424 1 86590509 86590523 COL24A1 0.013605442 X 65486260 65486271 HEPH 0.013605442 11 125763610 125763624 PUS3(NM_001271985: c.*70_*56del0, 0.013636364 NM_031307: c.*70_*56del0) 17 35988718 35988739 DDX52 0.01369863 11 94230106 94230131 ANKRD49 0.013793103 9 98009613 98009626 FANCC 0.013888889 2 70456452 70456465 TIA1 0.013888889 6 99817699 99817713 COQ3 0.013953488 4 140262240 140262251 NAA15 0.013986014 18 56279052 56279066 ALPK2 0.014018692 19 10097443 10097455 COL5A3 0.014052062 9 2083313 2083338 SMARCA2 0.014084507 X 129265852 129265866 AIFM1 0.014084507 2 208606875 208606908 CCNYL1 0.014084507 5 79369202 79369225 CTD-2201I18.1 0.014084507 17 65720150 65720161 NOL11 0.014084507 7 74608740 74608754 GTF2IP1, LOC100093631 0.014150943 16 66855468 66855480 NAE1 0.014184397 16 23486187 23486201 GGA2 0.014184397 4 99214537 99214549 RAP1GDS1 0.014285714 7 23761159 23761171 STK31 0.014285714 16 3828847 3828870 CREBBP 0.014388489 14 74426284 74426298 COQ6 0.014423077 X 153994469 153994482 DKC1 0.014440433 1 7912944 7912955 UTS2 0.014492754 5 158126222 158126236 EBF1 0.014492754 20 34435246 34435270 PHF20 0.014492754 5 101795499 101795510 SLCO6A1 0.014492754 9 100997485 100997498 TBC1D2 0.014545455 1 236737874 236737886 HEATR1 0.014563107 20 13140617 13140637 SPTLC3 0.01459854 21 40181937 40181956 ETS2 0.01459854 13 37011617 37011628 CCNA1 0.014634146 6 163899794 163899807 QKI 0.014705882 5 147793666 147793680 FBXO38 0.014705882 7 135304090 135304102 NUP205 0.014705882 3 101575877 101575895 NFKBIZ 0.014778325 X 52654536 52654550 SSX8 0.014778325 4 114176848 114176860 ANK2 0.014787278 13 111340025 111340053 CARS2 0.014801007 3 41877473 41877487 ULK4 0.014851485 2 175246386 175246411 CIR1 0.014851485 9 21861902 21861914 MTAP 0.014851485 6 146256315 146256344 SHPRH 0.014851485 X 108924091 108924121 ACSL4 0.014925373 6 39047035 39047052 GLP1R 0.014925373 1 75172756 75172771 CRYZ 0.014963067 10 102035182 102035193 BLOC1S2(NM_001282439: c.*37_*26del0, 0.015 NM_001282438: c.*37_*26del0, NM_001001342: c.*37_*26del0, NM_173809: c.*37_*26del0, NM_001282436: c.*37_*26del0, NM_001282437: c.*37_*26del0) 2 96994050 96994061 ITPRIPL1(NM_001008949: c.*13_*24del0, 0.015 NM_001163523: c.*13_*24del0, NM_178495: c.*13_*24del0, NM_001163524: c.*13_*24del0) 6 157496153 157496197 ARID1B 0.015037594 2 48046012 48046035 FBXO11 0.015037594 19 4430524 4430535 CHAF1A 0.015075377 6 109319962 109319991 SESN1 0.01509434 17 29206408 29206439 ATAD5 0.015209125 19 14153179 14153202 IL27RA 0.015267176 19 5727206 5727218 CATSPERD 0.015267176 14 35255287 35255316 BAZ1A 0.015267176 X 101409243 101409271 BEX5(NM_001159560: c.-6_-34del0, 0.01532567 NM_001012978: c.-6_-34del0) 13 79216356 79216381 RNF219 0.015384615 1 36297998 36298033 AGO4 0.015384615 6 34831755 34831773 UHRF1BP1 0.015463918 15 90229786 90229798 PEX11A 0.015503876 11 108332126 108332138 C11orf65 0.015503876 3 196236651 196236664 SMCO1 0.015503876 22 29879265 29879302 NEFH 0.015564202 X 132888207 132888236 GPC3 0.015564202 22 36872638 36872662 TXN2 0.015625 12 48880078 48880089 C12orf54 0.015625 1 200544650 200544673 KIF14 0.015655213 2 101885656 101885675 CNOT11 0.015686275 3 100438778 100438810 TFG 0.015706806 3 44399683 44399706 TCAIM 0.015706806 1 216373476 216373489 USH2A 0.015706806 3 3216976 3216988 CRBN 0.015716909 12 4645161 4645173 C12orf4 0.015873016 14 91633483 91633498 C14orf159 0.015873016 3 150906314 150906344 MED12L 0.015873016 3 38006175 38006186 CTDSPL 0.015873016 5 158630629 158630653 RNF145 0.015936255 11 108188266 108188280 ATM 0.015936255 2 110925982 110925995 NPHP1 0.015936255 8 53455013 53455024 FAM150A 0.015957447 3 121515940 121515953 IQCB1 0.016 X 119675354 119675368 CUL4B 0.016064257 13 100913132 100913161 PCCA 0.016064257 5 122359456 122359480 PPIC(NM_000943: c.*114_*90del0) 0.016129032 1 197898395 197898415 LHX9(NM_001014434: c.*6_*26del0, 0.016129032 NM_020204: c.*6_*26del0) 17 35620810 35620826 ACACA 0.016129032 14 74875955 74875968 SYNDIG1L 0.016161417 2 157370018 157370033 GPD2 0.016194332 2 24521686 24521697 ITSN2 0.016260163 12 88482779 88482791 CEP290 0.016260163 4 107037269 107037282 TBCK 0.016260163

TABLE 5 Microsatellite Repeat Marker Sequences for Lung Squamous Cell Carcinoma (LUSC). TABLE 5 - LUSC ch start_pos end_pos LUSC (hg37) (hg37) (hg37 gene p-value 3 48636506 48636516 UQCRC1(NM_003365: c.*55_*45del0) 1.42813E−10 X 53113895 53113905 TSPYL2 1.32824E−06 2 46583272 46583283 EPAS1 2.13437E−06 5 67584512 67584525 PIK3R1(NM_181524: c.-52_-39del-)  4.6354E−06 2 228159652 228159677 LOC654841 6.14867E−06 2 66796098 66796109 MEIS1  8.7468E−06 3 186295417 186295431 DNAJB11 1.30955E−05 17 67178976 67178992 ABCA10 1.55218E−05 2 179616770 179616786 TTN 2.19677E−05 13 73409508 73409522 PIBF1 2.39998E−05 1 155701055 155701071 DAP3 2.42228E−05 5 14485161 14485175 TRIO 2.87624E−05 17 67178764 67178794 ABCA10 3.10099E−05 15 50920509 50920523 TRPM7 3.64511E−05 2 215890346 215890382 ABCA12 4.20258E−05 18 43314395 43314412 SLC14A1 4.23846E−05 8 89499214 89499230 MMP16(dist = 159497), LOC101929709(dist = 1230397) 4.93243E−05 X 129354254 129354276 ZNF280C 5.65448E−05 11 124624705 124624721 ESAM 6.02149E−05 13 99890849 99890862 MIR548AN 6.16333E−05 10 63977011 63977030 RTKN2 6.18461E−05 1 169797067 169797078 C1orf112 6.57479E−05 6 100403812 100403827 MCHR2 7.86164E−05 3 108175734 108175745 MYH15 8.83002E−05 1 213180434 213180459 ANGEL2 9.06871E−05 9 20740346 20740366 FOCAD  9.7679E−05 3 185155430 185155442 MAP3K13 9.81082E−05 11 10820663 10820688 EIF4G2 0.000106296 6 43021976 43021989 MRPL2(NM_015950: c.*36_*23del0, 0.00011493 NM_001300848: c.*202_*189del0) 2 88484805 88484815 THNSL2 0.000116482 16 68155860 68155874 NFATC3 0.000133581 19 50911947 50911960 POLD1 0.000140056 2 21226218 21226230 APOB 0.000176336 X 100530312 100530326 TAF7L 0.000179631 2 175246545 175246557 CIR1 0.00019313 11 108121410 108121426 ATM 0.000194441 16 75674252 75674271 KARS 0.000201324 8 120800692 120800703 TAF2 0.000210393 1 211545442 211545459 TRAF5 0.000219138 20 4850568 4850578 SLC23A2 0.000220942 2 66670211 66670223 MEIS1 0.000221729 X 117883813 117883824 IL13RA1 0.000223964 21 17238572 17238582 USP25 0.000228781 18 77737714 77737726 TXNL4A 0.000230044 3 180679235 180679250 FXR1 0.000230044 15 41770598 41770624 RTF1 0.000230044 7 139097271 139097295 C7orf55-LUC7L2, LUC7L2 0.000233238 16 84907499 84907520 CRISPLD2 0.000261749 12 99117397 99117414 APAF1 0.000273332 4 187627659 187627676 FAT1 0.000274472 5 6623405 6623418 NSUN2 0.000278707 12 121004564 121004583 RNF10 0.000280306 17 35771517 35771528 TADA2A 0.000286862 9 19334957 19334970 DENND4C 0.00029264 2 110922055 110922080 NPHP1 0.000304553 15 52185961 52185975 TMOD3 0.000348334 10 27037487 27037499 ABI1 0.000388149 X 135080623 135080653 SLC9A6 0.000393465 19 11411997 11412010 TSPAN16 0.00040328 1 220369745 220369758 RAB3GAP2 0.000405725 11 104878040 104878051 CASP5 0.000407647 7 100319680 100319696 EPO 0.000418918 1 236737874 236737886 HEATR1 0.000432869 1 171511148 171511159 PRRC2C 0.000474083 12 120741303 120741326 SIRT4 0.000477669 12 31435608 31435620 FAM60A(NM_001135811: c.*38_*26del0, 0.000482952 NM_001135812: c.*38_*26del0, NM_021238: c.*38_*26del0) 12 125587478 125587491 AACS 0.000497512 7 101747593 101747605 CUX1 0.000502638 20 23473522 23473535 CST8 0.000509127 8 101933023 101933037 YWHAZ 0.000519211 6 64289938 64289954 PTP4A1 0.000543607 19 17366101 17366122 USHBP1 0.000544168 14 45497556 45497567 FAM179B 0.000549451 3 158407930 158407945 GFM1 0.00056684 13 52726707 52726730 NEK3 0.000568893 12 122437594 122437605 WDR66 0.000571102 6 157496153 157496197 ARID1B 0.000582411 10 12240681 12240702 CDC123 0.000583412 14 81448951 81448962 TSHR 0.000592107 15 42144967 42144979 SPTBN5 0.000594059 5 413428 413452 AHRR 0.000609595 11 128350396 128350418 ETS1 0.00061665 8 28707622 28707636 INTS9 0.000622665 2 179478746 179478757 MIR548N, TTN-AS1 0.000625586 12 107360876 107360887 TMEM263 0.000627707 7 20180425 20180476 MACC1(NM_182762: c.*144_*93del0) 0.000651972 18 67614674 67614695 CD226 0.000662659 17 39776817 39776829 KRT17 0.000670661 8 103287850 103287864 UBR5 0.000670661 15 66794298 66794311 RPL4 0.000677048 12 95488339 95488354 FGD6 0.000714213 3 47604262 47604281 CSPG5 0.000761905 3 184573472 184573483 VPS8 0.000766088 12 90005161 90005173 ATP2B1 0.000766812 9 86588185 86588199 HNRNPK 0.000769112 7 104747784 104747796 KMT2E 0.000774194 3 108224685 108224701 MYH15 0.000776972 20 16359356 16359369 KIF16B 0.000777717 9 98230924 98230947 LOC100507346 0.000784902 12 19475610 19475621 PLEKHA5 0.00079968 6 97615907 97615918 MIR548H3 0.000820793 1 202736222 202736233 KDM5B 0.000826674 8 37704283 37704295 BRF2 0.000826674 6 111685185 111685219 REV3L 0.000840336 20 36431202 36431215 CTNNBL1 0.000853339 2 176995682 176995693 HOXD8 0.000869187 19 9528423 9528438 ZNF266 0.000883002 1 46650191 46650201 TSPAN1 0.000926351 8 141293914 141293943 TRAPPC9 0.000938925 15 28427670 28427687 HERC2 0.00094156 13 50235208 50235218 EBPL 0.000949367 3 101575877 101575895 NFKBIZ 0.0009522 3 44815871 44815883 KIF15 0.000957854 8 12598316 12598327 LONRF1 0.000957854 21 43549808 43549820 UMODL1 0.000964295 1 153617510 153617526 CHTOP 0.000964721 6 97000341 97000356 UFL1 0.000975515 19 37155495 37155509 ZNF461 0.000985011 11 107904512 107904524 CUL5 0.000994554 12 64491002 64491019 SRGAP1 0.001046296 5 158630629 158630653 RNF145 0.001055276 2 55883509 55883523 PNPT1 0.001056636 5 70809269 70809285 BDP1 0.001083686 4 70280786 70280798 UGT2B28(dist = 120018), UGT2B4(dist = 65085) 0.001093534 X 3539376 3539390 PRKX 0.001098901 6 100988266 100988280 ASCC3 0.001122209 6 151859146 151859161 CCDC170 0.001125407 6 32147291 32147312 RNF5P1 0.00113342 3 113377481 113377493 KIAA2018 0.001136105 6 137325901 137325917 IL20RA 0.001139212 2 207013834 207013846 NDUFS1 0.001145288 21 46602483 46602497 ADARB1 0.001162308 7 102727051 102727067 ARMC10 0.001182033 5 132408905 132408918 HSPA4 0.001194172 11 59368218 59368235 OSBP 0.001211924 1 160302354 160302365 COPA 0.001220575 14 75199555 75199568 FCF1 0.00122489 15 83808031 83808046 HDGFRP3 0.001228555 3 179298584 179298597 ACTL6A 0.001236858 15 72244247 72244286 MYO9A 0.001240145 2 170917983 170917996 UBR3 0.001249844 17 7726648 7726698 DNAH2 0.001267579 10 13633928 13633944 PRPF18 0.001274968 17 39976721 39976731 FKBP10 0.001297641 3 130733046 130733058 ASTE1 0.001300632 17 34151245 34151260 TAF15 0.001360421 3 57850505 57850518 SLMAP 0.001393035 6 111702448 111702460 REV3L 0.001403153 17 57762402 57762414 CLTC 0.001413708 3 160131236 160131250 SMC4 0.001457224 11 108549186 108549200 DDX10 0.001495647 1 65129233 65129268 CACHD1 0.001495647 1 36884530 36884544 OSCP1 0.001534319 2 136527318 136527332 UBXN4 0.001543125 3 38938299 38938322 SCN11A 0.001579511 15 50570999 50571024 GABPB1 0.001603849 2 64139831 64139844 VPS54 0.001630435 5 55034756 55034770 DDX4 0.001645123 13 111932586 111932617 ARHGEF7 0.001699958 11 134064516 134064540 NCAPD3 0.001708817 2 186689258 186689269 FSIP2 0.001708817 7 73666736 73666750 RFC2 0.001715717 20 55206241 55206253 TFAP2C 0.001718846 7 56126036 56126047 CCT6A 0.00172117 19 53905129 53905144 ZNF765 0.001731836 5 64084746 64084771 CWC27 0.001761597 15 70961809 70961821 UACA 0.001805986 3 48491343 48491366 ATRIP 0.001806215 7 92129161 92129183 PEX1 0.00181686 20 41306488 41306500 PTPRT 0.001854305 6 152539326 152539345 SYNE1 0.001858494 15 50873112 50873154 TRPM7 0.001858494 3 10018739 10018754 EMC3 0.001877006 2 15676703 15676717 NBAS 0.00188383 22 46679850 46679864 TTC38 0.001885133 12 66531936 66531947 TMBIM4 0.001941371 4 187560860 187560871 FAT1 0.00194742 14 31191658 31191682 SCFD1 0.001970046 9 15458080 15458092 SNAPC3 0.001983544 12 107237602 107237626 RIC8B 0.001984018 18 59942586 59942600 KIAA1468 0.002011494 14 104145625 104145642 KLC1 0.002063242 13 28133956 28133972 LNX2 0.00212999 6 134494708 134494722 SGK1 0.002307337 10 12215870 12215884 NUDT5 0.002394913 17 9501525 9501545 CFAP52 0.002419744 17 57278908 57278920 PRR11 0.002445031 14 31762500 31762511 HEATR5A 0.002451559 17 5324558 5324611 RPAIN 0.002457002 2 36986088 36986108 VIT 0.002457002 10 81036869 81036879 ZMIZ1 0.002596054 12 104714847 104714867 TXNRD1 0.002631729 10 64975001 64975012 JMJD1C 0.002667088 5 68413042 68413072 SLC30A5 0.002677702 2 56102061 56102072 EFEMP1 0.002695418 1 45472798 45472829 HECTD3 0.002700187 2 27463091 27463105 CAD 0.002713704 2 54163830 54163905 PSME4 0.002754337 12 104515109 104515121 NFYB 0.002757078 7 103206001 103206013 RELN 0.002925697 18 649879 649895 TYMSOS(NM_001012716: c.*120_*104del0) 0.002963439 1 103471456 103471487 COL11A1 0.003078376 2 207027356 207027368 EEF1B2 0.003081827 12 21327652 21327667 SLCO1B1 0.003081827 7 133881908 133881936 LRGUK 0.003221819 10 61956386 61956407 ANK3 0.003266874 5 63803508 63803522 RGS7BP 0.00330263 X 135292012 135292028 FHL1 0.003378378 17 5044640 5044653 USP6 0.003392501 17 28773060 28773074 CPD 0.003410796 14 35899480 35899493 NFKBIA(dist = 25520), INSM2(dist = 103755) 0.003411857 1 89449508 89449520 RBMXL1 0.003496503 8 37611414 37611428 ERLIN2 0.003517546 5 139936680 139936694 SRA1 0.003544037 16 90141288 90141302 PRDM7 0.003704708 5 134032954 134032965 SEC24A 0.003764412 1 14057425 14057439 PRDM2 0.003795385 21 34655334 34655346 IL10RB 0.003806927 15 55972660 55972674 PRTG 0.003850113 22 41545024 41545039 EP300 0.003850165 13 111340025 111340053 CARS2 0.003891377 10 75214137 75214149 PPP3CB 0.003894145 10 116203903 116203928 ABLIM1 0.004034497 15 25319287 25319304 SNORD116-10 0.004039951 5 94903575 94903589 ARSK 0.004058202 3 132179072 132179085 DNAJC13 0.004077817 2 183832100 183832113 NCKAP1 0.004104649 15 102287989 102288000 TARSL2(dist = 23344), OR4F6(dist = 57923) 0.004130466 1 170927570 170927588 MROH9 0.004172571 1 173797451 173797462 DARS2 0.004172571 5 137507104 137507121 BRD8 0.004173092 3 113376110 113376147 KIAA2018 0.0042042 11 88068256 88068270 CTSC 0.004274795 12 69090573 69090587 NUP107 0.004406754 11 118247264 118247277 UBE4A 0.004409435 12 43826277 43826290 ADAMTS20 0.004427021 10 28872473 28872498 WAC 0.004545455 7 95818864 95818897 SLC25A13 0.004591776 6 24412431 24412445 MRS2 0.004598134 6 46636556 46636581 SLC25A27 0.004634401 7 24789116 24789134 DFNA5 0.00466523 8 68139326 68139338 ARFGEF1 0.00472565 9 2083313 2083338 SMARCA2 0.004834508 8 110334770 110334782 NUDCD1 0.004868549 4 114176848 114176860 ANK2 0.004937786 18 18619416 18619428 ROCK1 0.004970882 11 102272460 102272474 TMEM123 0.005094144 4 48381682 48381704 SLAIN2 0.005096981 11 108058769 108058785 NPAT 0.005097955 12 50867998 50868014 LARP4 0.005102041 1 215914883 215914896 USH2A 0.005224756 2 86998651 86998676 RMND5A 0.005230322 7 20826270 20826284 SP8 0.005235602 9 32485288 32485313 DDX58 0.00544955 19 5739320 5739333 CATSPERD 0.005494505 15 74536285 74536301 CCDC33 0.005541183 1 24180806 24180833 FUCA1 0.005558934 10 76349020 76349033 ADK 0.005603164 7 5567254 5567271 ACTB(NM_001101: c.*125_*108del0) 0.005649718 16 22271671 22271685 EEF2K 0.00566619 5 81601142 81601155 ATP6AP1L(NM_001017971: c.-79_-66del-) 0.005747126 X 24084241 24084254 EIF2S3 0.005820582 12 6858889 6858905 MLF2 0.005843734 5 176729736 176729749 RAB24 0.005881775 6 90366329 90366347 LOC101929057 0.005894638 17 80443296 80443308 NARF 0.005913256 9 85987879 85987892 FRMD3 0.006035135 19 55501348 55501365 NLRP2 0.006565027 20 46266543 46266558 NCOA3 0.006672895 10 101731593 101731631 DNMBP 0.006756757 15 48717850 48717884 FBN1 0.006896552 16 67409030 67409054 LRRC36 0.006944444 8 95750744 95750759 DPY19L4 0.006944444 17 54981571 54981588 TRIM25 0.007076105 7 75513199 75513231 RHBDD2 0.007142857 1 52403174 52403187 RAB3B 0.007142857 5 162945387 162945400 MAT2B(NM_182796: c.*18_*31del0, 0.007188258 NM_013283: c.*18_*31 del0) 1 101194965 101194977 VCAM1 0.007225164 14 95999676 95999689 SNHG10 0.007260544 12 14599896 14599919 ATF7IP 0.007308175 5 7885782 7885795 MTRR 0.007374771 6 90347394 90347406 LYRM2 0.007633588 8 117864952 117864973 RAD21 0.007633588 16 69293926 69293945 SNTB2 0.007664042 8 120580546 120580569 ENPP2 0.007664725 1 67516191 67516202 SLC35D1 0.007878914 1 213009178 213009196 SPATA45 0.007959728 14 35497274 35497286 SRP54 0.008049905 10 34985197 34985210 PARD3 0.008080842 X 153216185 153216195 HCFC1 0.008130081 15 45446084 45446109 DUOX1 0.008151034 4 91549147 91549168 CCSER1 0.00823979 8 139380103 139380130 FAM135B 0.008264463 10 26825151 26825168 APBB1IP 0.008322941 1 207679180 207679198 CRI 0.008474576 10 94366347 94366370 KIF11 0.008522708 10 105990647 105990660 CFAP43 0.00862069 5 158526517 158526550 EBF1(NM_024007: c.-31_-64del0, 0.008624591 NM_001290360: c.-31_-64del0, NM_182708: c.-31_-64del0) 17 33998753 33998764 AP2B1 0.00872633 13 20056698 20056716 TPTE2 0.008928571 5 58021809 58021820 RAB3C 0.009009009 4 1806012 1806024 FGFR3 0.009021513 X 40588550 40588561 MED14 0.009250243 1 33135035 33135055 RBBP4 0.009345794 2 203384776 203384799 BMPR2 0.009345794 1 98011812 98011842 DPYD 0.00937633 1 181714466 181714481 CACNA1E 0.009405926 X 109416688 109416703 TMEM164(NM_017698: c.*9_*24del0, 0.009416538 NM_032227: c.*9_*24del0) 1 63096855 63096873 DOCK7 0.009433962 20 29623380 29623389 FRG1B 0.00952381 17 45105631 45105644 RPRML(dist = 49017), ARL17A(dist = 3308) 0.009615385 7 86823977 86823988 DMTF1 0.009615385 14 96848565 96848580 GSKIP 0.009708738 2 99936265 99936280 TXNDC9 0.01 X 135328309 135328320 MAP7D3 0.01010101 5 31435975 31435987 DROSHA 0.010309278 1 39352116 39352127 RHBDL2(NM_017821: c.*60_*49del0) 0.010309278 7 154745910 154745921 PAXIP1 0.010309278 9 740769 740788 KANK1 0.010356963 15 41060070 41060085 DNAJC17(NM_018163: c.*68_*53del0) 0.010416667 19 23845789 23845807 ZNF675 0.010416667 X 15364158 15364186 PIR-FIGF 0.010416667 15 43784435 43784447 RNU6-28P 0.010425965 2 211521213 211521243 CPS1 0.01052978 17 12920526 12920549 ELAC2 0.010638298 16 19063220 19063235 TMC7 0.010658937 12 31820564 31820578 METTL20 0.010928962 2 162081128 162081140 TANK 0.010928962 7 138951165 138951177 UBN2 0.011049724 12 27841925 27841938 PPFIBP1 0.0110951 13 73636910 73636929 KLF5 0.01110156 16 67470052 67470095 HSD11B2 0.011111111 2 222290623 222290635 EPHA4(NM_004438: c.*125_*113del0) 0.011235955 17 35538304 35538314 ACACA 0.011235955 12 1909656 1909667 CACNA2D4 0.011363636 18 19110456 19110477 ESCO1 0.011378114 17 39723415 39723439 KRT9 0.011477574 5 147785802 147785816 FBXO38 0.011558576 2 86348737 86348749 PTCD3 0.011560694 14 74426284 74426298 COQ6 0.011976048 16 5129689 5129703 ALG1 0.012121212 7 94042504 94042515 COLLA2 0.012195122 2 10928694 10928709 PDIA6 0.012259994 1 113159364 113159384 ST7L 0.012269939 2 178364328 178364342 AGPS 0.012577028 1 168205770 168205781 SFT2D2 0.012578616 6 148761410 148761421 SASH1 0.012658228 2 238925144 238925166 UBE2F-SCLY 0.012738854 18 29238076 29238091 B4GALT6 0.012794551 22 26886953 26886982 SRRD 0.01282012 9 70993092 70993104 PGM5 0.012866192 5 146773709 146773725 DPYSL3 0.012903226 2 58362150 58362161 VRK2 0.012987013 5 94206957 94206971 MCTP1 0.012987013 12 112515954 112515966 NAA25 0.012987013 11 66618396 66618426 PC 0.013071895 14 59790749 59790763 DAAM1 0.013157895 11 102080325 102080341 YAP1 0.013288501 8 131193153 131193166 ASAP1 0.013314349 5 37326073 37326084 NUP155 0.013333333 14 89878206 89878246 FOXN3 0.013333333 3 192516152 192516163 MB21D2(NM_178496: c.*23_*12del0) 0.013333333 10 70252822 70252837 SLC25A16 0.013422819 2 219341717 219341730 USP37 0.013513514 5 179150788 179150800 CANX 0.013605442 12 31289662 31289674 DDX11(dist = 31937), FAM60A(dist = 143846) 0.013605442 19 7707445 7707455 STXBP2 0.013753651 2 101581294 101581308 NPAS2 0.013764251 15 54586266 54586278 UNC13C 0.013784009 X 83403148 83403160 RPS6KA6 0.013888889 7 103828911 103828922 ORC5 0.013888889 18 180211 180228 USP14 0.014048048 17 28811834 28811848 GOSR1 0.014084507 14 93686568 93686587 UBR7 0.014182614 19 47656338 47656359 SAE1 0.014184397 1 32119347 32119376 COL16A1 0.014459225 9 8338847 8338866 PTPRD 0.014470918 10 111651598 111651609 XPNPEP1 0.01459854 11 86120270 86120294 CCDC81 0.014705882 12 989800 989815 WNK1 0.01476888 11 67209167 67209194 CORO1B 0.014925373 13 53239754 53239767 SUGT1 0.015037594 5 36123065 36123135 LMBRD2 0.015151515 4 7817686 7817710 AFAP1 0.0152262 10 5788110 5788126 FAM208B 0.015294739 20 37126168 37126180 RALGAPB 0.015384615 10 32327037 32327053 KIF5B 0.015503876 6 70966421 70966435 COL9A1 0.015639415 6 89614390 89614408 RNGTT 0.015748031 8 124244005 124244016 C8orf76, ZHX1-C8orf76 0.015873016 19 6013202 6013215 LOC100128568 0.015873016 13 98634737 98634749 IPO5 0.016042781 14 74443828 74443841 ENTPD5 0.016129032 16 67286352 67286366 SLC9A5 0.016393443 5 70805272 70805288 BDP1 0.016445815 2 230656987 230657001 TRIP12 0.016483516 1 211280724 211280748 KCNH1 0.016496612 3 58296209 58296232 RPP14 0.016496612 7 98630574 98630598 LOC101927550 0.016528926 1 154144673 154144694 TPM3 0.016666667 9 96209987 96209999 FAM120AOS 0.016770111 1 236590675 236590687 EDARADD 0.016806723 2 25656889 25656901 DTNB 0.016839036 5 32057910 32057923 PDZD2 0.016949153 17 79176010 79176020 CEP131 0.016949153 11 126174242 126174254 DCPS 0.016949153 12 111160513 111160526 PPP1CC 0.017045455 2 165365365 165365376 GRB14 0.017241379 3 196532148 196532160 PAK2 0.017241379 7 97939975 97939988 BAIAP2L1 0.017241379 19 53277686 53277727 ZNF600 0.017241379 1 36282435 36282452 AGO4 0.017241379 1 183873947 183873965 RGL1 0.017391304 1 217784431 217784441 GPATCH2 0.017408801 5 50122645 50122660 PARP8 0.01754386 2 10095014 10095031 GRHL1 0.01754386 14 96794877 96794890 ATG2B 0.017699115 2 32983299 32983311 TTC27 0.017699115 1 173921292 173921316 RC3H1 0.017857143 15 44057632 44057645 PDIA3 0.018018018 14 89037482 89037493 ZC3H14 0.018119102 4 99214537 99214549 RAP1GDS1 0.018181818 14 50121442 50121460 POLE2 0.018181818 12 109510086 109510099 USP30 0.018292683 2 11317833 11317856 PQLC3 0.018348624 19 52646629 52646648 ZNF616(dist = 3438), ZNF836(dist = 11477) 0.018351539 11 28113094 28113107 KIF18A 0.018404908 16 71808499 71808519 AP1G1 0.018404908 13 25839869 25839885 MTMR6 0.018404908 12 14599855 14599867 ATF7IP 0.018518519 14 90499389 90499401 TDP1 0.018518519 5 98208016 98208027 CHD1 0.018518519 19 42933173 42933197 LIPE-AS1 0.018518519 13 33637913 33637928 KL 0.018592703 14 96770942 96770967 ATG2B 0.018625096 14 64460536 64460551 SYNE2 0.018630567 14 73959703 73959720 C14orf169(NM_024644: c.*56_*73del0) 0.018683428 20 35695535 35695562 RBL1 0.018691589 3 121720514 121720530 ILDR1 0.01872207 12 88566358 88566370 TMTC3 0.01875 12 107398862 107398876 CRY1 0.018867925 15 41364265 41364305 INO80 0.018867925 14 39620884 39620896 TRAPPC6B 0.018867925 6 129955151 129955165 ARHGAP18 0.018984235 16 70693872 70693884 IL34 0.018990299 20 62163783 62163814 PTK6 0.01910828 21 44513110 44513140 U2AF1(NM_001025204: c.*102_*72del0, 0.019230769 NM_006758: c.*102_*72del0, NM_001025203: c.*102_*72del0) 1 114186351 114186362 MAGI3 0.019230769 9 3937244 3937266 GLIS3 0.019230769 13 108518658 108518714 FAM155A 0.019230769 3 111873902 111873917 SLC9C1 0.019247877 12 89995053 89995065 ATP2B1 0.019354839 21 47821449 47821460 PCNT 0.019417476 12 27803097 27803114 PPFIBP1 0.019417476 11 65268479 65268492 MALAT1 0.019480519 4 52928352 52928371 SPATA18 0.019488012 14 69861462 69861490 ERH 0.019607843 12 78594396 78594427 NAV3 0.01980198 3 143551065 143551076 SLC9A9 0.01980198 12 57677520 57677531 R3HDM2 0.01980198 6 56869464 56869475 BEND6 0.01986755 12 69980447 69980462 CCT2 0.019900498 9 33062183 33062195 SMU1 0.02 5 88018305 88018317 MEF2C(NM_001193350: c.*116_*104del0, 0.02 NM_001131005: c.*116_*104del0, NM_002397: c.*116_*104del0, NM_001193347: c.*116_*104del0, NM_001193348: c.*116_*104del0, NM_001193349: c.*116_*104del0) 18 60034075 60034100 TNFRSF11A 0.02 1 100174683 100174709 MIR548AA1, MIR548D1 0.02 16 58585178 58585191 CNOT1 0.020134228 11 49196555 49196567 FOLH1 0.020134228 2 101185539 101185550 PDCL3 0.020134228 5 162884074 162884113 NUDCD2 0.02020202 1 7912944 7912955 UTS2 0.02020202 3 100569452 100569464 ABI3BP 0.02020202 16 51176119 51176131 SALL1 0.020408163 1 15890342 15890359 DNAJC16 0.020417133 7 35189891 35189905 DPY19L2P1 0.020833333 15 42536227 42536238 TMEM87A 0.020833333 13 25355954 25355978 RNF17 0.020833333 4 54319247 54319262 FIP1L1 0.020833333 12 111701486 111701497 CUX2 0.020933775 1 151380720 151380737 POGZ 0.021052632 12 2997058 2997074 RHNO1 0.021052632 9 2088640 2088651 SMARCA2 0.021052632 4 155457781 155457826 PLRG1(NM_002669: c.*56_*11del0, 0.021052632 NM_001201564: c.*56_*11del0) 3 170715672 170715694 SLC2A2 0.021126761 3 24270412 24270424 THRB 0.021276596 1 22030891 22030902 USP48 0.021276596 21 42823193 42823206 MX1 0.021276596 6 144179190 144179202 LTV1 0.021276596 2 45645684 45645695 SRBD1 0.021276596 6 54791345 54791356 FAM83B 0.021276596 1 151010849 151010872 BNIPL 0.021276596 19 19308821 19308837 RFXANK 0.021276596 5 179032860 179032871 RUFY1 0.021390374 7 7572355 7572381 COL28A1 0.021390374 19 15511205 15511221 AKAP8L 0.021447254 18 30913142 30913153 CCDC178 0.021505376 17 17796875 17796886 TOM1L2 0.021505376 14 53213128 53213140 STYX 0.021582734 16 30665449 30665465 PRR14 0.021621622 2 45806939 45806979 SRBD1 0.021645022

TABLE 6 Microsatellite Repeat Marker Sequences for Rectum Adenocarcinoma (READ). TABLE 6 - READ ch start_pos end_pos READ (hg37) (hg37 (hg37) gene p-value 10 112360315 112360333 SMC3 8.22741E−07 16 3808052 3808066 CREBBP 9.18755E−07 X 19380975 19380993 MAP3K15 9.18755E−07 11 118885668 118885701 CCDC84 9.18755E−07 5 36123065 36123135 LMBRD2 1.02919E−06 10 35314130 35314161 CUL2 1.22792E−06 6 122733490 122733508 HSF2 1.22792E−06 12 125587478 125587491 AACS 1.30467E−06 8 33356825 33356839 MAK16(NM_032509: c.*678_*692del0) 1.79261E−06 7 97939975 97939988 BAIAP2L1 2.05071E−06 12 110834030 110834049 ANAPC7 2.24629E−06 6 102130410 102130422 GRIK2  2.3498E−06 9 75420448 75420463 TMC1 2.48475E−06 13 79216356 79216381 RNF219 2.53158E−06 19 6026288 6026302 RFX2 2.85868E−06 17 29508819 29508836 NF1 3.00528E−06 16 9010826 9010844 USP7  3.1614E−06 4 146031236 146031253 ABCE1 3.16205E−06 X 106092450 106092473 TBC1D8B 3.50527E−06 12 100496478 100496498 UHRF1BP1L  3.9732E−06 3 113442784 113442795 NAA50  4.0016E−06 12 89853387 89853405 POC1B  4.1137E−06 5 172578549 172578567 BNIP1 4.24695E−06 15 55841195 55841209 PYGO1 4.34216E−06 1 222904869 222904881 BROX 4.59377E−06 3 41877473 41877487 ULK4 4.62695E−06 12 85285920 85285938 SLC6A15(NM_182767: c.-21 _-39del0, 4.62695E−06 NM_018057: c.-21_-39del0) 10 64022582 64022593 RTKN2 5.13927E−06 9 52625 52641 FAM138C(dist = 16761), PGM5P3-AS1(dist = 20049) 5.14597E−06 6 46636556 46636581 SLC25A27 5.78368E−06 8 53543090 53543106 RB1CC1 5.78368E−06 8 100160282 100160300 VPS13B 5.83216E−06 16 10567751 10567778 ATF7IP2  6.1396E−06 2 8998775 8998788 MBOAT2(NM_138799: c.*34_*21del0)  6.1396E−06 1 149900985 149901002 MTMR11(NM_001145862: c.*36_*19del0) 6.52333E−06 2 141294271 141294299 LRP1B 6.52333E−06 2 203676382 203676403 ICAIL 6.73886E−06 6 49415351 49415368 MUT 6.93751E−06 2 32095023 32095056 MEMO1 7.86936E−06 6 36452603 36452620 KCTD20 8.39398E−06 11 47701629 47701642 AGBL2 9.58121E−06 17 57937792 57937807 TUBD1 9.98335E−06 16 75674252 75674271 KARS 1.02536E−05 4 120423686 120423697 PDE5A 1.02536E−05 13 28133956 28133972 LNX2 1.09421E−05 9 79968285 79968309 VPS13A  1.0986E−05 8 24348425 24348437 LOC101929294, LOC101929315 1.17849E−05 6 44364261 44364277 CDC5L 1.21579E−05 14 36218039 36218056 RALGAPA1P 1.23411E−05 4 76528928 76528945 CDKL2 1.26579E−05 1 93687513 93687543 CCDC18 1.30364E−05 2 120714401 120714418 PTPN4 1.31447E−05 10 115380483 115380497 NRAP 1.36132E−05 4 39501722 39501754 MIR1273H 1.37813E−05 17 30687599 30687612 ZNF207 1.58102E−05 3 33893929 33893949 PDCD6IP 1.64818E−05 15 55972660 55972674 PRTG  1.7411E−05 6 96971185 96971208 UFL1 1.82682E−05 12 121618278 121618293 P2RX7 1.84188E−05 20 58497481 58497497 SYCP2(NM_014258: c.-13_-29del0) 1.92694E−05 3 130733046 130733058 ASTE1 1.99537E−05 3 33626219 33626236 CLASP2 2.18531E−05 2 196762491 196762509 DNAH7 2.27026E−05 3 169992958 169992994 PRKCI 2.28938E−05 12 129360344 129360381 GLT1D1 2.35987E−05 7 137076100 137076123 DGKI 2.40015E−05 5 180481216 180481233 BTNL9 2.51819E−05 2 207013834 207013846 NDUFS1 2.51819E−05 21 37706087 37706100 MORC3 2.51819E−05 3 52696310 52696322 PBRM1  2.6441E−05 8 109462215 109462229 EMC2 2.69354E−05 2 55883509 55883523 PNPT1 2.77855E−05 15 52571270 52571284 MYO5C 2.77855E−05 14 104465128 104465144 TDRD9 2.80324E−05 2 211527815 211527840 CPS1 2.80324E−05 14 20344373 20344394 OR4K2 2.81976E−05 9 91083260 91083278 SPIN1 3.03143E−05 13 73409508 73409522 PIBF1 3.06401E−05 2 99936265 99936280 TXNDC9 3.07607E−05 4 99214537 99214549 RAP1GDS1 3.07607E−05 15 59693969 59693985 MYO1E(dist = 28898), FAM81A(dist = 36387) 3.07607E−05 11 110306734 110306760 FDX1 3.29579E−05 5 145647187 145647210 RBM27 3.41763E−05 12 57032216 57032235 ATP5B  3.6075E−05 7 92900502 92900527 CCDC132 3.68321E−05 19 12574740 12574762 ZNF709(NM_152601: c.*70_*48del0) 3.68321E−05 1 176050430 176050447 RFWD2  3.8117E−05 4 141481203 141481225 UCP1 3.88222E−05 12 109510086 109510099 USP30 4.03161E−05 12 78594396 78594427 NAV3 4.14008E−05 9 98009613 98009626 FANCC 4.21035E−05 12 123703074 123703086 MPHOSPH9 4.26876E−05 20 3245219 3245232 C20orf194 4.41424E−05 22 30051705 30051722 NF2 4.51671E−05 6 116911413 116911425 RWDD1 4.52489E−05 X 2343183 2343213 DHRSX 4.72337E−05 20 57569617 57569636 NELFCD 4.86855E−05 5 58270446 58270485 PDE4D(NM_001197223: c.*45_*6del0,  5.6899E−05 NM_001197221: c.*45_*6del0, NM_001197220: c.*45_*6del0, NM_001165899: c.*45_*6del0, NM_001197218: c.*45_*6del0, NM_001197222: c.*45_*6del0, NM_001197219: c.*45_*6del0, NM_006203: c.*45_*6del0, NM_001104631: c.*45_*6del0) 5 14485161 14485175 TRIO  5.6899E−05 3 5249962 5249976 EDEM1 5.71588E−05 X 118679315 118679331 CXorf56 5.78168E−05 15 30010328 30010349 TJP1 6.17055E−05 1 115280193 115280207 CSDE1 6.17055E−05 4 95508108 95508128 PDLIM5 6.17055E−05 14 36096255 36096278 RALGAPA1P 6.17055E−05 6 142691950 142691968 GPR126 6.17055E−05 3 37176656 37176670 LRRFIP2 6.43128E−05 6 89638988 89639004 RNGTT 6.43128E−05 14 60587879 60587900 PCNXL4 6.43128E−05 13 31195409 31195432 USPL1 6.43128E−05 2 197654578 197654593 GTF3C3 6.58762E−05 17 40880759 40880775 EZH1 6.99851E−05 3 111873902 111873917 SLC9C1  7.1775E−05 2 212578379 212578394 ERBB4 7.21521E−05 20 35695535 35695562 RBL1 7.30727E−05 1 25679278 25679290 TMEM50A 7.30727E−05 5 86629039 86629073 RASA1 7.30727E−05 12 56504143 56504159 PA2G4 7.63446E−05 1 33402334 33402352 RNF19B(NM_001127361: c.*555_*537del0, 7.63446E−05 NM_153341: c.*73_*55del0, NM_001300826: c.*73_*55del0) 15 64496611 64496630 CSNK1G1 7.70891E−05 1 47123898 47123914 ATPAF1 7.77863E−05 21 19653342 19653355 TMPRSS15 7.98148E−05 16 47399670 47399687 ITFG1 7.98148E−05 1 231094050 231094067 TTC13 7.98148E−05 6 99817699 99817713 COQ3 7.98148E−05 1 22033369 22033411 USP48 7.98148E−05 22 42415224 42415240 WBP2NL 8.10307E−05 1 94964139 94964155 ABCD3 8.24946E−05 1 63128836 63128850 DOCK7 8.34986E−05 16 24185815 24185831 PRKCB 8.34986E−05 5 169020337 169020350 SPDL1 8.34986E−05 2 141625834 141625854 LRP1B 8.34986E−05 4 166215662 166215692 KLHL2 8.34986E−05 15 43170667 43170727 TTBK2 8.34986E−05 7 81695842 81695859 CACNA2D1 8.46197E−05 2 110922055 110922080 NPHP1  8.7108E−05 20 47649496 47649525 ARFGEF2 8.74126E−05 2 110325590 110325602 SEPT10 9.15751E−05 10 13633928 13633944 PRPF18 9.15751E−05 1 150676674 150676692 HORMAD1 9.15751E−05 1 52242432 52242447 OSBPL9 9.15751E−05 1 169819526 169819538 C1orf112 9.15751E−05 11 49196555 49196567 FOLH1 9.19202E−05 17 58289521 58289533 USP32 9.38086E−05 1 216495186 216495197 USH2A 9.38086E−05 8 131193153 131193166 ASAP1 9.52925E−05 5 178030941 178030955 CLK4 9.60061E−05 2 136677957 136677968 DARS 9.60061E−05 12 50152601 50152618 TMBIM6 9.77135E−05 16 90141288 90141302 PRDM7 0.000100728 6 70459209 70459222 LMBRD1 0.000101215 12 66522628 66522660 LLPH 0.000105764 15 43307839 43307852 UBR1 0.000106666 4 146076632 146076644 OTUD4 0.000107871 16 21623935 21623964 METTL9 0.000108836 8 109247189 109247210 EIF3E 0.000108836 7 26883761 26883776 SKAP2 0.000109421 8 28707622 28707636 INTS9 0.000111142 1 92763091 92763128 GLMN 0.000111142 21 37706065 37706077 MORC3 0.000111142 3 138248009 138248026 CEP70 0.000111142 20 37191391 37191408 RALGAPB 0.000111142 2 179595571 179595589 TTN 0.000111142 9 103027226 103027243 INVS 0.000112918 6 11714639 11714665 ADTRP(NM_001143948: c.*72_*46del0, 0.000114893 NM_032744: c.*72_*46del0) 13 48664556 48664569 MED4 0.000116891 3 146177594 146177608 PLSCR2 0.000116891 5 33546113 33546143 ADAMTS12 0.000116891 10 26802633 26802648 APBB1IP 0.000116891 6 133108763 133108784 SLC18B1 0.000116891 22 40755427 40755439 ADSL 0.000116891 18 40503735 40503751 RIT2 0.000121546 11 59368218 59368235 OSBP 0.000121714 3 129168854 129168881 IFT122 0.000121714 5 38958956 38958971 RICTOR 0.000123043 7 105122891 105122924 PUS7 0.000123043 14 64460536 64460551 SYNE2 0.000129634 3 179083024 179083036 MFN1 0.000129634 8 75157416 75157442 JPH1 0.000136705 14 35550467 35550490 LOC101927178 0.000136705 12 124281419 124281436 DNAH10 0.000137554 20 10273694 10273715 SNAP25 0.000142248 12 96694172 96694190 CDK17 0.000142248 2 48046012 48046035 FBXO11 0.0001443 8 67759411 67759438 C8orf44-SGK3, SGK3 0.0001443 5 86679495 86679514 RASA1 0.0001443 11 49088577 49088602 TRIM64C(dist = 7913), FOLH1(dist = 79585) 0.0001443 18 19119813 19119828 ESCO1 0.000148093 5 150846858 150846882 SLC36A1 0.000152468 15 33218472 33218487 FMN1 0.000154264 14 58825825 58825847 ARID4A 0.000160511 9 30689085 30689104 LINC01242(dist = 280633), ACO1(dist = 1695497) 0.000160782 X 101409243 101409271 BEX5(NM_001159560: c.-6_-34del0, 0.000160782 NM_001012978: c.-6_-34del0) 20 480602 480627 CSNK2A1 0.000161264 5 151180439 151180475 G3BP1 0.000161264 8 141754888 141754905 PTK2 0.000161264 2 15753307 15753321 DDX1 0.000161264 16 53913911 53913925 FTO 0.000161264 12 51752085 51752103 GALNT6 0.000164517 8 23712066 23712089 STC1(NM_003155: c.-30_-53del0) 0.000167673 15 83805209 83805222 TM6SF1 0.000167673 10 12226870 12226882 NUDT5 0.00017075 15 40062813 40062836 FSIP1 0.00017075 14 55231286 55231297 SAMD4A 0.00017075 22 39079920 39079936 TOMM22(NM_020243: c.*74_*90del0) 0.000174963 16 20749284 20749296 THUMPD1 0.000180995 5 134011834 134011848 SEC24A 0.000182256 7 36465606 36465622 ANLN 0.000182682 6 80910611 80910635 BCKDHB 0.000183284 2 158275111 158275135 CYTIP 0.000190862 1 32381592 32381607 PTP4A2 0.000190862 4 141448696 141448718 ELMOD2 0.000190862 16 46652286 46652305 SHCBP1 0.000190862 X 119675354 119675368 CUL4B 0.000192077 5 78608348 78608371 JMY 0.000192077 8 133984814 133984834 TG 0.000199537 1 93691855 93691881 CCDC18 0.000199537 1 197053561 197053577 ASPM 0.000199537 2 86683539 86683575 KDM3A 0.000199537 9 79835312 79835353 VPS13A 0.000199537 1 39900058 39900076 MACF1 0.000204082 9 131715001 131715017 NUP188 0.000208213 7 35218768 35218786 DPY19L2P1 0.000208746 7 21603750 21603765 DNAH11 0.000208746 14 96794877 96794890 ATG2B 0.000217108 17 30267579 30267601 SUZ12 0.000217108 5 145888687 145888714 TCERG1 0.000217673 7 92020452 92020465 ANKIB1 0.000218531 9 133498017 133498047 FUBP3 0.000218531 5 96093391 96093408 CAST 0.000218531 17 19744865 19744877 ULK2 0.000222469 19 9361740 9361752 OR7E24 0.000225258 21 33979904 33979922 C21orf59 0.000229564 2 60988862 60988872 PAPOLG 0.000231267 9 88287588 88287615 AGTPBP1 0.000231267 9 86354663 86354679 GKAP1 0.000234412 12 104077096 104077126 STAB2 0.000234412 2 103343275 103343295 MFSD9 0.000234412 3 14696955 14696967 CCDC174 0.000240015 2 179407763 179407779 MIR548N, TTN-AS1 0.000246685 18 66367726 66367742 TMX3 0.000246685 1 163313695 163313707 NUF2 0.000246685 17 29195444 29195460 ATAD5 0.000251819 12 12974842 12974853 DDX47 0.000251819 5 10394911 10394930 MARCH6 0.000252912 12 97306603 97306631 NEDD1 0.000262895 16 31202698 31202716 FUS 0.000262895 3 113169372 113169386 SPICE1 0.000262895 3 160144007 160144039 SMC4 0.000263505 12 43964612 43964623 ADAMTS20(dist = 18888), PUS7L(dist = 157787) 0.000263505 3 97605460 97605472 CRYBG3 0.00026441 3 113377481 113377493 KIAA2018 0.00026441 8 48732074 48732096 PRKDC 0.00026441 3 183558468 183558512 PARL 0.00026441 2 201778717 201778733 ORC2 0.000273411 2 157352734 157352747 GPD2 0.000276853 2 219341717 219341730 USP37 0.000277855 2 128854948 128854963 UGGTI 0.000277855 3 180320897 180320910 TTC14 0.000281889 1 207237233 207237262 PFKFB2 0.000281889 12 112119387 112119420 BRAP 0.000284495 4 113506885 113506900 ZGRF1 0.000289019 14 55636060 55636079 DLGAP5 0.000289019 1 245025697 245025717 HNRNPU 0.000292227 5 67584512 67584525 PIK3R1(NM_181524: c.-52_-39del-) 0.000301908 16 23457290 23457308 COG7 0.000301908 X 48214185 48214200 SSX3 0.000302024 8 120856021 120856034 DSCC1 0.00030525 10 88458996 88459025 LDB3 0.00030525 5 37027560 37027590 NIPBL 0.000307607 6 149846372 149846387 PPIL4 0.000315576 5 35068814 35068826 PRLR 0.000315576 6 157495951 157495966 ARID1B 0.000316456 13 48828102 48828118 ITM2B 0.000321564 1 175087683 175087694 TNN 0.000324086 20 13140617 13140637 SPTLC3 0.000324123 6 165809963 165809979 PDE10A 0.000324123 7 2406737 2406755 EIF3B 0.000324123 14 103915242 103915254 MARK3 0.000324123 14 35242702 35242726 BAZ1A 0.000335345 6 36569717 36569737 SRSF3 0.000335345 2 64139831 64139844 VPS54 0.000341763 6 33408890 33408917 SYNGAP1 0.00034188 14 96770942 96770967 ATG2B 0.000343013 4 76997157 76997173 ART3 0.000345488 2 239241445 239241460 TRAF3IP1 0.000345488 10 89720622 89720649 PTEN 0.000345488 20 33033065 33033083 ITCH 0.000348432 5 61745737 61745750 IPO11 0.000348432 12 73012649 73012663 TRHDE 0.000349926 5 172421760 172421776 ATP6V0E1 0.000359749 1 33087567 33087584 ZBTB8OS 0.000361869 14 102550069 102550088 HSP90AA1 0.000381723 11 48970767 48970782 OR4A47(dist = 459493), TRIM49B(dist = 82370) 0.000381723 5 65372793 65372805 ERBB2IP 0.000392454 16 15159022 15159039 PDXDC1, RRN3 0.000397573 1 170927570 170927588 MROH9 0.000397875 12 94575162 94575177 PLXNC1 0.000399074 4 119674051 119674062 SEC24D 0.000403161 21 40650627 40650652 BRWD1 0.000403161 2 66796098 66796109 MEIS1 0.000403161 5 36629801 36629815 SLC1A3 0.000404858 2 91887905 91887919 LOC654342(dist = 39930), GGT8P(dist = 75449) 0.000404858 5 162884074 162884113 NUDCD2 0.000414079 16 69293926 69293945 SNTB2 0.000417493 11 108141955 108141971 ATM 0.000417679 6 75890933 75890959 COL12A1 0.000428961 3 10018739 10018754 EMC3 0.000434783 1 114495348 114495383 HIPK1 0.000437063 19 33406199 33406229 CEP89 0.000438819 14 65472874 65472892 MAX(NM_001271069: c.*48_*30del0, 0.000442092 NM_197957: c.*48_*30del0) 2 48734331 48734349 PPP1R21 0.000443095 9 5811331 5811349 ERMP1 0.000452489 3 10103903 10103946 FANCD2 0.000452489 1 63270823 63270838 ATG4C 0.000457875 13 43872451 43872468 ENOX1 0.000459807 4 25366051 25366071 ZCCHC4 0.000461411 13 26151184 26151196 ATP8A2 0.0004662 21 33312539 33312554 HUNK 0.0004662 7 99796751 99796765 STAG3 0.0004662 15 82517622 82517671 EFTUD1 0.000474158 2 45806939 45806979 SRBD1 0.000474158 7 77584159 77584171 PHTF2 0.000480031 1 233225957 233225969 PCNXL2 0.000480192 6 42611936 42611951 UBR2 0.000480769 6 117725383 117725399 ROS1 0.000480769 8 104075165 104075177 ATP6V1C1 0.000480769 12 28412398 28412416 CCDC91 0.00048558 1 79383748 79383762 ELTDI 0.000489837 6 49815873 49815888 CRISP1 0.000494071 10 17204246 17204272 TRDMT1 0.000494968 2 160092703 160092716 WDSUB1 0.000496032 14 59787325 59787338 DAAM1 0.000496032 6 71571688 71571707 SMAP1(NM_001281439: c.*1751_*1770del0, 0.000496032 NM_021940: c.*1651_*1670del0, NM_001044305: c.*1651_*1670del0, NM_001281440: c.*1651_*1670del0) 17 39522910 39522922 KRT33B 0.000496032 4 17841869 17841881 NCAPG 0.000503639 17 1265304 1265326 YWHAE 0.000510204 10 76349020 76349033 ADK 0.000511467 2 209195472 209195485 PIKFYVE 0.000512033 9 125655308 125655324 RC3H2 0.000512033 2 66670211 66670223 MEIS1 0.000512033 9 102730697 102730712 STX17 0.000514801 11 58892376 58892387 FAM111B 0.000514801 12 104714847 104714867 TXNRD1 0.000535737 3 121202433 121202476 POLQ 0.000535737 6 131948816 131948831 MED23 0.000539227 21 27136460 27136473 GABPA 0.000546448 9 7128277 7128289 KDM4C 0.000546448 3 93754286 93754317 ARL13B 0.00055571 4 89352469 89352487 HERC6 0.00055571 1 215824195 215824226 USH2A 0.000560224 18 67613932 67613959 CD226 0.000560224 4 128814425 128814449 PLK4 0.000564972 19 10741681 10741697 SLC44A2 0.000568355 18 67614674 67614695 CD226 0.000578168 5 118500981 118501000 DMXL1 0.000578168 12 45771901 45771918 ANO6 0.000580032 17 46190093 46190110 SNX11 0.000580032 2 38216766 38216779 RMDN2-AS1 0.000580032 3 112253193 112253208 ATG3 0.000582798 17 10317164 10317176 MYHAS 0.000584454 7 107875143 107875165 NRCAM 0.000584454 4 25315637 25315653 ZCCHC4 0.000594177 2 111406968 111406984 BUB1 0.000601076 2 169994021 169994058 LRP2 0.000604961 1 118502087 118502108 WDR3(NM_006784: c.*17_*38del0) 0.000604961 4 170658944 170658956 C40rf27 0.000604961 3 156411774 156411807 TIPARP 0.000604961 12 64491002 64491019 SRGAPI 0.000611154 13 51522081 51522094 RNASEH2B 0.000611154 13 43491778 43491796 EPSTII 0.000615214 13 39608335 39608360 PROSERI 0.000626566 8 67969596 67969610 COPS5 0.000626566 X 133511862 133511890 PHF6 0.000626566 1 74901739 74901760 FPGT-TNNI3K, TNNI3K 0.000629347 3 38257551 38257583 OXSR1 0.000635571 19 38282490 38282505 ZNF573(dist = 12260), LOC644554(dist = 25546) 0.000639386 16 21809188 21809208 RRN3P1 0.000649351 6 42626564 42626585 UBR2 0.000656111 1 173797451 173797462 DARS2 0.000658762 8 107704921 107704955 OXR1 0.000672757 1 186330695 186330709 MIR548F1 0.000672757 5 147785802 147785816 FBXO38 0.000673401 6 88853530 88853542 CNR1(NM_001160259: c.*45_*33del0, 0.000673401 NM_001160226:c.*45_*33del0, NM_001160258: c.*45_*33del0, NM_033181: c.*45_*33del0, NM_016083: c.*45_*33del0) 14 91365646 91365664 RPS6KA5 0.000673401 5 122714134 122714153 CEP120 0.000698812 3 113166840 113166859 SPICE1 0.000698812 15 80460576 80460591 FAH 0.000704722 16 56535193 56535208 BBS2 0.000708569 2 101885656 101885675 CNOT11 0.000721501 9 77550305 77550323 TRPM6(dist = 47295), C9orf40(dist = 11176) 0.000721501 17 66904031 66904045 ABCA8 0.000725241 5 118487582 118487593 DMXL1 0.000725689 4 55976947 55976961 KDR 0.000734536 12 64679694 64679708 C12orf56 0.000746095 9 37887570 37887587 SLC25A51 0.000746095 16 31284618 31284634 ITGAM 0.00075188 7 149543201 149543232 ZNF862 0.000754148 13 29238622 29238633 POMP 0.000754148 4 44691795 44691810 GUF1 0.00076234 20 55206241 55206253 TFAP2C 0.000784314 6 111685185 111685219 REV3L 0.000784314 9 128064242 128064260 GAPVD1 0.0008033 10 43199666 43199677 LINC01518(dist = 12459), BMS1(dist = 78277) 0.000806452 11 122928926 122928953 HSPA8 0.000816273 8 80831393 80831407 MRPS28 0.000816327 X 11793084 11793105 MSL3 0.000816327 3 172052897 172052914 FNDC3B 0.000846203 4 128812230 128812245 PLK4 0.000853313 5 72185591 72185607 TNPO1 0.000853313 9 133498229 133498245 FUBP3 0.000853313 2 196738263 196738274 DNAH7 0.00087108 17 43587579 43587591 LRRC37A4P 0.000886525 12 81239721 81239737 LIN7A 0.000893596 2 179548695 179548712 TTN 0.000893596 3 19498221 19498253 KCNH8 0.000925069 13 115011550 115011564 CDC16 0.000936453 17 28773060 28773074 CPD 0.000936453 1 92108274 92108288 CDC7(dist = 116953), TGFBR3(dist = 37612) 0.000936453 16 15702117 15702141 KIAA0430 0.000938086 1 132179950 132179979 NTM 0.000945257 7 151921037 151921049 KMT2C 0.000949367 8 130874614 130874639 FAM49B 0.000966184 18 77737714 77737726 TXNL4A 0.000966184 18 21046255 21046274 RIOK3 0.000966184 13 23808732 23808745 SGCG 0.000969921 10 30605169 30605182 MTPAP 0.00097371 1 86435957 86435971 COL24A1 0.000982096 15 73580950 73580962 NEO1 0.000982096 9 130127691 130127703 GARNL3 0.000982096 2 219350358 219350383 USP37 0.000982096 3 12571420 12571434 TSEN2(NM_001145395: c.*9_*23del0) 0.000999001 12 30887772 30887832 CAPRIN2 0.001010101 3 65361369 65361402 MAGI1 0.001010101 1 241954005 241954024 WDR64 0.001011122 1 220284112 220284124 RNU5F-1 0.001012146 9 115060090 115060107 MIR3134 0.001012146 13 42772765 42772789 DGKH 0.00102529 5 141520013 141520031 NDFIP1 0.00102529 1 65099701 65099716 CACHD1 0.001030752 11 35287000 35287014 SLC1A2 0.001030752 17 11697015 11697027 DNAH9 0.001030752 11 14539315 14539332 PSMA1 0.001036258 18 649879 649895 TYMSOS(NM_001012716: c.*120_*104del0) 0.001052632 2 99614595 99614609 TSGA10(NM_025244: c.*65_*51del0, 0.001052632 NM_182911: c.*65_*51del0) 20 13695824 13695839 ESF1 0.001052632 19 40587849 40587876 ZNF780A 0.001057082 1 151134579 151134590 LYSMD1, TNFAIP8L2-SCNM1 0.001057082 11 86120270 86120294 CCDC81 0.001060391 1 173490547 173490571 SLC9C2 0.001081081 X 110494528 110494543 CAPN6 0.001082676 1 220355521 220355533 RAB3GAP2 0.001082676 1 117605130 117605145 TTF2 0.001086518 13 25911034 25911067 NUPL1 0.001094212 4 187627659 187627676 FAT1 0.001094691 18 30913142 30913153 CCDC178 0.00110742 1 24973106 24973116 SRRM1 0.00110742 1 23650293 23650315 HNRNPR 0.00110742 11 59626477 59626491 TCN1 0.00110742 8 35401930 35401941 UNC5D 0.00110742 6 32147291 32147312 RNF5P1 0.0011107 2 230656987 230657001 TRIP12 0.001141553 1 155701055 155701071 DAP3 0.001141553 19 55044241 55044256 KIR3DX1 0.001141553 12 416046 416060 KDM5A 0.00116144 2 11332238 11332250 ROCK2 0.001173709 3 180679235 180679250 FXR1 0.001173709 1 155884155 155884167 KIAA0907 0.001173709 11 108549186 108549200 DDX10 0.001173709 5 55034756 55034770 DDX4 0.001185396 7 116556086 116556111 CAPZA2 0.001185396 12 91372042 91372059 EPYC 0.001185771 1 196709736 196709747 CFH 0.001185995 7 123332378 123332391 WASL 0.001207243 12 124144572 124144584 GTF2H3 0.001219512 6 52400479 52400497 TRAM2 0.001221001 14 50760968 50760980 L2HGDH 0.001221001 2 61462921 61462939 USP34 0.001221001 4 42626659 42626674 ATP8A1 0.00123354 10 34573008 34573020 PARD3 0.001242236 15 63447932 63447960 RPS27L 0.001242236 8 101253085 101253108 SPAG1 0.001242236 19 327260 327277 MIER2 0.001260989 10 74874082 74874112 NUDT13 0.001260989 3 167045701 167045723 ZBBX 0.001260989 1 198717210 198717235 PTPRC 0.001262626 3 158526942 158526966 MFSD1 0.001278772 13 111932586 111932617 ARHGEF7 0.001278772 5 7896957 7896969 MTRR 0.001278772 7 8110836 8110848 GLCCI1 0.001282051 2 196912236 196912247 DNAH7 0.001282051 13 114113737 114113748 DCUN1D2 0.001282051 5 94842718 94842730 TTC37 0.001297641 7 139097271 139097295 C7orf55-LUC7L2, LUC7L2 0.001316945 8 71037103 71037115 NCOA2 0.001316945 7 135375909 135375932 SLC13A4 0.001316945 2 208606875 208606908 CCNYL1 0.001316945 7 72879898 72879914 BAZ1B 0.001316945 2 62063093 62063111 FAM161A 0.00132908 6 15651642 15651656 DTNBP1 0.00132908 5 158126222 158126236 EBF1 0.00132908

TABLE 7 Microsatellite Repeat Marker Sequences for Stomach Adenocarcinoma (STAD). TABLE 7 - STAD ch start_pos end_pos STAD (hg37) (hg37) (hg37) gene p-value 19 14104688 14104703 RFX1(NM_002918: c.-33_-48del0) 1.28727E−45 7 102727051 102727067 ARMC10 9.55899E−44 7 74608740 74608754 GTF2IP1, LOC100093631 1.13938E−42 6 64289938 64289954 PTP4A1 1.81433E−42 3 10018739 10018754 EMC3 4.68392E−42 22 46679850 46679864 TTC38 2.43723E−40 3 5249962 5249976 EDEM1 2.75634E−40 12 122017894 122017916 KDM2B 9.66091E−40 20 37146131 37146146 RALGAPB 1.03207E−39 13 28133956 28133972 LNX2 2.02103E−39 11 117152291 117152314 RNF214 2.17143E−39 2 120714401 120714418 PTPN4 1.11316E−38 21 34117067 34117080 PAXBP1 3.95934E−38 8 103287850 103287864 UBR5  1.031E−37 12 95488339 95488354 FGD6  1.8452E−37 6 157495951 157495966 ARID1B 2.11186E−37 1 116940481 116940497 ATP1A1-AS1 2.29381E−37 2 64112697 64112719 UGP2 3.10569E−37 11 118369265 118369290 KMT2A 1.30605E−36 6 32147291 32147312 RNF5P1 1.66973E−36 16 75674252 75674271 KARS 2.86736E−36 3 172052897 172052914 FNDC3B 4.26236E−36 8 120856021 120856034 DSCC1 5.16378E−36 12 122762763 122762779 CLIP1 6.15345E−36 15 41770639 41770652 RTF1 6.19935E−36 19 327260 327277 MIER2 6.98054E−36 10 70056619 70056632 PBLD 1.44221E−35 9 97555228 97555242 C9orf3 1.63642E−35 19 11565819 11565831 ELAVL3 1.90189E−35 9 131456159 131456172 SET 2.31906E−35 15 42503953 42503965 TMEM87A 2.94397E−35 7 7572355 7572381 COL28A1  3.289E−35 12 125587478 125587491 AACS 3.89995E−35 13 48664556 48664569 MED4 4.07756E−35 4 128814425 128814449 PLK4 4.67887E−35 12 51323672 51323684 METTL7A 4.70829E−35 10 26825151 26825168 APBB1IP 6.26346E−35 22 35719378 35719394 TOM1 6.68163E−35 13 79216356 79216381 RNF219  1.1357E−34 14 51348281 51348299 ABHD12B 1.24803E−34 22 41545024 41545039 EP300 1.87092E−34 7 65426054 65426069 GUSB 2.18258E−34 4 8472785 8472805 TRMT44 3.41232E−34 12 99117397 99117414 APAF1 3.69336E−34 2 207027356 207027368 EEF1B2 4.00635E−34 X 129267464 129267478 AIFM1  4.3021E−34 10 17110577 17110588 CUBN 4.65827E−34 18 60025458 60025474 TNFRSF11A 5.11943E−34 17 30500816 30500828 RHOT1 6.40288E−34 2 228680153 228680168 CCL20 8.57126E−34 20 36431202 36431215 CTNNBL1 9.80737E−34 18 649879 649895 TYMSOS(NM_001012716: c.*120_*104del0) 1.02753E−33 X 12994867 12994886 TMSB4X 1.03104E−33 2 175246545 175246557 CIR1 1.13971E−33 13 99890849 99890862 MIR548AN 1.39515E−33 12 132539500 132539513 EP400 1.52667E−33 2 48046012 48046035 FBXO11 1.59709E−33 1 14057425 14057439 PRDM2 2.44452E−33 2 179407763 179407779 MIR548N, TTN-AS1 2.98376E−33 6 165809963 165809979 PDE10A 3.16757E−33 4 128812230 128812245 PLK4 3.63777E−33 3 121720514 121720530 ILDR1 3.80152E−33 1 222904869 222904881 BROX 5.06052E−33 6 111329221 111329239 RPF2 8.31212E−33 12 48360947 48360961 TMEM106C 9.87843E−33 13 113965002 113965017 LAMP1 1.18782E−32 7 150918586 150918602 ABCF2 1.21597E−32 5 33561022 33561043 ADAMTS12  1.487E−32 22 30772228 30772244 KIAA1656 1.60835E−32 3 113377481 113377493 KIAA2018 1.67704E−32 X 118679315 118679331 CXorf56 2.22403E−32 8 95186510 95186526 CDH17 2.28161E−32 8 133984814 133984834 TG 2.38561E−32 5 55034756 55034770 DDX4 2.66771E−32 2 61308569 61308585 KIAA1841 3.01141E−32 17 73515055 73515068 TSEN54 3.03314E−32 1 151384052 151384067 POGZ  3.0501E−32 7 26883761 26883776 SKAP2  3.1717E−32 4 113107829 113107845 C4orf32 3.63708E−32 11 8486375 8486389 STK33 4.19111E−32 2 228159652 228159677 LOC654841 4.33298E−32 2 61577667 61577680 USP34 4.72874E−32 20 33338325 33338339 NCOA6  5.9106E−32 8 124822507 124822519 FAM91A1 6.04363E−32 17 57278908 57278920 PRR11  6.5616E−32 3 121515940 121515953 IQCB1 7.18008E−32 15 30010328 30010349 TJP1 7.28827E−32 2 110922055 110922080 NPHP1 7.29612E−32 8 80831393 80831407 MRPS28 7.73674E−32 7 139097271 139097295 C7orf55-LUC7L2, LUC7L2 8.06811E−32 12 104714847 104714867 TXNRD1 8.99373E−32 14 64443258 64443278 MIR548AZ 1.08002E−31 6 64419024 64419039 PHF3 1.16932E−31 1 94964139 94964155 ABCD3 1.24921E−31 7 92900502 92900527 CCDC132 1.29611E−31 10 101992923 101992938 CWF19L1(NM_018294: c.*61_*46del0) 1.70679E−31 20 60587772 60587788 TAF4 1.72119E−31 5 14485161 14485175 TRIO  1.7941E−31 4 151850226 151850239 LRBA 2.54944E−31 12 133375066 133375092 GOLGA3 2.84218E−31 5 147785802 147785816 FBXO38  2.9737E−31 7 138270744 138270757 TRIM24 3.46508E−31 2 32117217 32117230 MEMO1 3.69556E−31 1 22030115 22030132 USP48 3.94101E−31 19 50911947 50911960 POLD1 4.11486E−31 19 9771286 9771300 ZNF562 4.58568E−31 7 33217071 33217084 BBS9 4.70048E−31 15 80460576 80460591 FAH 5.92599E−31 1 84956161 84956173 RPF1 7.07072E−31 6 13316780 13316795 TBC1D7 7.77151E−31 5 78416973 78416990 BHMT 9.53115E−31 1 44805012 44805054 ERI3  1.0275E−30 1 150932953 150932989 SETDB1 1.06404E−30 6 56504477 56504489 RNU6-71P 1.14019E−30 10 103567665 103567680 MGEA5 1.22417E−30 1 86435957 86435971 COL24A1 1.27042E−30 6 128330423 128330435 PTPRK 1.46169E−30 2 62063093 62063111 FAM161A 1.54421E−30 3 180320897 180320910 TTC14 1.55368E−30 8 104922508 104922534 RIMS2 1.71751E−30 8 30569609 30569622 GSR 1.72395E−30 3 138193025 138193038 ESYT3 1.92985E−30 2 64331815 64331833 PELI1 1.93697E−30 10 118891992 118892021 VAX1 2.02847E−30 2 234178624 234178640 ATG16L1 2.56955E−30 X 129546260 129546274 RBMX2 3.04384E−30 6 15651642 15651656 DTNBP1 3.09992E−30 17 66039938 66039951 KPNA2  3.3665E−30 4 83970297 83970312 COPS4 3.54802E−30 4 119666217 119666241 SEC24D 3.70716E−30 9 102730697 102730712 STX17 4.73147E−30 9 15472611 15472623 PSIP1 6.13511E−30 1 153949135 153949147 JTB 6.16896E−30 8 74204423 74204438 RPL7 7.77021E−30 2 10928694 10928709 PDIA6 7.83205E−30 17 15973417 15973449 NCOR1 8.37048E−30 8 130874614 130874639 FAM49B 8.91674E−30 8 38940143 38940157 ADAM9 9.20495E−30 8 142161666 142161681 DENND3 1.12727E−29 17 66038979 66038999 KPNA2 1.18635E−29 20 46266543 46266558 NCOA3 1.21007E−29 15 55972660 55972674 PRTG  1.3928E−29 12 98989187 98989199 SLC25A3 1.59855E−29 2 120620092 120620108 PTPN4 1.60176E−29 12 104461711 104461723 HCFC2 1.67358E−29 15 43927623 43927636 CATSPER2 1.69383E−29 8 68140383 68140394 ARFGEF1 1.81641E−29 1 78432506 78432521 FUBP1 1.90834E−29 1 3549854 3549874 WRAP73 2.36714E−29 5 70837260 70837275 BDP1 2.50137E−29 5 134015495 134015508 SEC24A 2.52438E−29 2 79314062 79314073 REG1B 2.58249E−29 19 6026288 6026302 RFX2 2.88305E−29 14 104145625 104145642 KLC1 2.94657E−29 11 59626477 59626491 TCN1 2.95675E−29 6 116914112 116914128 RWDD1 3.50117E−29 7 152144203 152144216 FABP5P3(dist = 4103), LINC01003(dist = 16993) 3.89354E−29 5 94842718 94842730 TTC37 4.10289E−29 1 175116046 175116071 TNN 4.99251E−29 11 47187055 47187087 ARFGAP2 5.04417E−29 9 19334957 19334970 DENND4C  5.1499E−29 2 34907636 34907654 GART  5.5525E−29 6 163899794 163899807 QKI  5.6508E−29 11 74053485 74053497 PGM2L1 6.42335E−29 8 62550924 62550938 ASPH 6.49943E−29 6 42611936 42611951 UBR2 6.58913E−29 6 36452603 36452620 KCTD20 6.60275E−29 4 17841869 17841881 NCAPG 6.81996E−29 3 19959707 19959719 EFHB 7.11458E−29 9 131743701 131743715 NUP188 7.20219E−29 X 134025421 134025436 MOSPD1 7.59034E−29 2 39240584 39240596 SOS1 7.77384E−29 2 111406968 111406984 BUB1 8.93529E−29 17 74729588 74729600 METTL23 1.03849E−28 3 57850505 57850518 SLMAP 1.07548E−28 17 8417006 8417020 MYH10 1.07706E−28 12 64491002 64491019 SRGAP1 1.26622E−28 16 4559351 4559367 HMOX2 1.28267E−28 1 41456808 41456823 CTPS1 1.30576E−28 17 66041871 66041886 KPNA2 1.46969E−28 13 26151184 26151196 ATP8A2 1.62391E−28 1 63128836 63128850 DOCK7 1.63257E−28 8 37611414 37611428 ERLIN2 1.75926E−28 11 124624705 124624721 ESAM 2.02752E−28 11 124007701 124007714 VWA5A 2.03767E−28 8 23712066 23712089 STC1(NM_003155: c.-30_-53del0) 2.05249E−28 12 4645161 4645173 C12orf4  2.0984E−28 6 25452453 25452466 LRRC16A 2.12232E−28 7 92020452 92020465 ANKIB1 2.12232E−28 2 70456452 70456465 TIA1  2.2463E−28 7 135099044 135099059 CNOT4 2.35627E−28 11 73984657 73984669 P4HA3 2.43161E−28 9 135773000 135773019 TSC1 2.55479E−28 10 32575773 32575785 EPC1 2.71151E−28 10 74899343 74899356 ECD 2.75224E−28 1 89449508 89449520 RBMXL1 2.88271E−28 14 88407716 88407730 GALC 2.98955E−28 10 115380483 115380497 NRAP 2.99401E−28 10 116605738 116605750 FAM160B1 3.08154E−28 X 135115669 135115681 SLC9A6 3.53796E−28 9 163927 163943 CBWD1 3.61255E−28 7 94989255 94989273 PON3(NM_000940: c.*30_*12del0) 3.63573E−28 3 191888452 191888477 FGF12 3.64344E−28 6 90366329 90366347 LOC101929057  4.1867E−28 2 112854563 112854576 TMEM87B 4.37261E−28 8 67759411 67759438 C8orf44-SGK3, SGK3  4.7387E−28 11 108121410 108121426 ATM 5.06994E−28 5 93294451 93294463 FAM172A 5.12501E−28 12 53861636 53861650 PCBP2 5.85829E−28 13 39608335 39608360 PROSER1 5.87731E−28 8 141293914 141293943 TRAPPC9  5.9086E−28 3 62153593 62153621 PTPRG 6.02936E−28 19 36145409 36145425 COX6B1 6.23563E−28 3 48491343 48491366 ATRIP 6.34319E−28 8 131193153 131193166 ASAP1 6.58505E−28 11 125488247 125488261 STT3A 6.99352E−28 12 104515109 104515121 NFYB 7.41136E−28 4 25315637 25315653 ZCCHC4 7.52201E−28 5 172578549 172578567 BNIP1  9.4251E−28 1 145456732 145456747 NBPF10, NBPF20, POLR3GL 9.85339E−28 11 59368218 59368235 OSBP 1.11222E−27 15 101550861 101550877 LRRK1 1.12118E−27 5 74011541 74011556 HEXB 1.13187E−27 7 74119460 74119488 LOC101926943 1.14187E−27 13 73409508 73409522 PIBF1 1.22983E−27 2 64069277 64069293 UGP2(NM_006759: c.-43_-27del-) 1.35367E−27 X 100532479 100532505 TAF7L 1.41147E−27 12 57882764 57882777 MARS 1.46143E−27 4 108935768 108935822 HADH 1.84961E−27 2 201534173 201534187 AOX1 2.23824E−27 4 114176848 114176860 ANK2 2.25481E−27 12 107237602 107237626 RIC8B  2.2592E−27 17 1326754 1326769 CRK(NM_005206: c.*183_*168del0, 2.43472E−27 NM_016823: c.*53_*38del0) 11 47701629 47701642 AGBL2 2.60331E−27 16 69293926 69293945 SNTB2 2.81142E−27 9 17464479 17464491 CNTLN 2.82293E−27 8 28707622 28707636 INTS9 2.93586E−27 19 34945331 34945344 UBA2 3.15202E−27 12 123703074 123703086 MPHOSPH9 3.20538E−27 8 37704283 37704295 BRF2 3.66865E−27 2 74754818 74754830 AUP1 3.86606E−27 20 7921106 7921120 HAO1 4.20796E−27 3 158407930 158407945 GFM1 4.69517E−27 15 25319287 25319304 SNORD116-10 4.74832E−27 17 57762402 57762414 CLTC 4.86717E−27 17 44409890 44409927 LRRC37A 4.88321E−27 9 80343587 80343612 GNAQ 4.97372E−27 21 30435646 30435668 CCT8 5.32326E−27 3 71008341 71008362 FOXP1(NM_001244816: c.*57_*36del0, 5.42766E−27 NM_001244812: c.*57_*36del0, NM_001244813: c.*57_*36del0, NM_001244808: c.*57_*36del0, NM_001244815: c.*57_*36del0, NM_001244814: c.*57_*36del0, NM_032682: c.*57_*36del0, NM_001244810: c.*57_*36del0) 1 167871297 167871312 ADCY10 5.53076E−27 16 84907499 84907520 CRISPLD2 5.84658E−27 2 101885656 101885675 CNOT11 5.99198E−27 5 150282674 150282694 ZNF300 6.38016E−27 5 140076413 140076436 HARS2  6.8234E−27 16 57249981 57250000 RSPRY1 7.02244E−27 3 160134195 160134221 SMC4 7.09839E−27 10 5788110 5788126 FAM208B 7.41558E−27 16 19063220 19063235 TMC7 7.43645E−27 5 70809269 70809285 BDPI 7.51021E−27 1 173795803 173795821 DARS2 7.77883E−27 12 56500502 56500515 PA2G4 7.87435E−27 13 111340025 111340053 CARS2 8.22896E−27 15 45725103 45725138 C15orf48 9.03216E−27 15 50596341 50596355 GABPB1 1.01324E−26 13 50586051 50586064 DLEU2 1.06985E−26 4 113568126 113568140 LARP7 1.13001E−26 2 211179765 211179777 MYL1 1.16606E−26 11 63149670 63149682 SLC22A9 1.17544E−26 5 147793666 147793680 FBXO38 1.20732E−26 15 72875521 72875535 ARIH1 1.22861E−26 5 178030941 178030955 CLK4 1.26563E−26 X 48214185 48214200 SSX3 1.40426E−26 2 27463091 27463105 CAD 1.67084E−26 3 146177594 146177608 PLSCR2 1.71727E−26 19 47700438 47700453 SAE1 1.74952E−26 6 31832356 31832372 SLC44A4  1.8027E−26 6 30619285 30619302 C6orf136 1.85971E−26 2 204156968 204156980 CYP20A1 1.88602E−26 2 128263363 128263377 IWS1  1.902E−26 5 180481216 180481233 BTNL9 1.92591E−26 2 47635523 47635537 MSH2 2.04143E−26 5 82937251 82937262 HAPLN1(NM_001884: c.*64_*53del0) 2.23621E−26 9 99408079 99408094 AAED1 2.29568E−26 1 150799125 150799138 ARNT 2.38177E−26 13 45973231 45973246 SLC25A30 2.45175E−26 2 175246386 175246411 CIR1 2.57125E−26 17 54981571 54981588 TRIM25 2.62816E−26 4 52928352 52928371 SPATA18 2.69973E−26 7 106523362 106523383 PIK3CG 2.76304E−26 19 21350520 21350533 ZNF431 2.89881E−26 20 34430474 34430486 PHF20 2.90299E−26 17 62748076 62748093 LOC146880  2.9926E−26 3 185155430 185155442 MAP3K13 3.07057E−26 3 33725814 33725828 CLASP2 3.50466E−26 2 136527318 136527332 UBXN4 3.55504E−26 15 41060070 41060085 DNAJC17(NM_018163: c.*68_*53del0)  3.5814E−26 15 83808031 83808046 HDGFRP3 3.60952E−26 14 91372685 91372700 RPS6KA5 3.63751E−26 12 107398862 107398876 CRY1 3.68736E−26 14 31191658 31191682 SCFD1 3.75564E−26 1 92763091 92763128 GLMN 3.88999E−26 1 116655183 116655197 MAB21L3(NM_152367: c.-54_-40del-) 3.89624E−26 1 207753824 207753846 CR1 4.64132E−26 14 102476130 102476143 DYNC1H1 4.86995E−26 11 118883880 118883892 CCDC84 5.13074E−26 13 39435552 39435564 FREM2 5.16696E−26 12 90005161 90005173 ATP2B1 5.48804E−26 2 120366057 120366070 CFAP221 6.27043E−26 1 202736222 202736233 KDM5B 6.48588E−26 1 155671899 155671929 DAP3 6.67349E−26 12 31435608 31435620 FAM60A(NM_001135811: c.*38_*26del0, 6.74389E−26 NM_001135812: c.*38_*26del0, NM_021238: c.*38_*26del0) 16 19619602 19619617 C16orf62 6.92793E−26 5 139907750 139907762 ANKHD1, ANKHD1-EIF4EBP3 7.16687E−26 2 197654578 197654593 GTF3C3 7.58006E−26 13 77644856 77644877 MYCBP2 7.84163E−26 11 65268479 65268492 MALAT1 8.25136E−26 7 102825987 102826001 DPY19L2P2 8.58113E−26 7 75651305 75651336 STYXL1 8.74332E−26 3 30691871 30691882 TGFBR2 9.14943E−26 14 65472874 65472892 MAX(NM_001271069: c.*48_*30del0,  9.3654E−26 NM_197957: c.*48_*30del0) 9 127287158 127287183 NR6A1 1.13275E−25 11 22296094 22296106 ANO5 1.20729E−25 1 220284112 220284124 RNU5F-1 1.23682E−25 17 57937792 57937807 TUBD1 1.34815E−25 3 123332875 123332892 MYLK-AS1 1.34868E−25 2 15676703 15676717 NBAS 1.35141E−25 15 43307839 43307852 UBR1  1.3818E−25 2 48032740 48032754 MSH6 1.48442E−25 6 55739711 55739726 BMP5(NM_021073: c.-48_-63del0) 1.65309E−25 12 73012649 73012663 TRHDE 1.66273E−25 16 3808052 3808066 CREBBP 1.69752E−25 8 67969596 67969610 COPS5 1.71665E−25 3 5024415 5024435 BHLHE40 1.72335E−25 6 137325901 137325917 IL20RA 1.83349E−25 8 127595047 127595058 FAM84B(dist = 24336), PCAT1(dist = 430341) 1.91057E−25 7 138434066 138434081 ATP6V0A4 1.97563E−25 14 20763824 20763838 TTC5 2.28252E−25 1 54252939 54252952 NDC1 2.46911E−25 8 38839302 38839316 HTRA4  2.4758E−25 11 17526254 17526267 USH1C 2.54098E−25 4 76997157 76997173 ART3 2.56062E−25 19 14153179 14153202 IL27RA 2.61144E−25 3 108224685 108224701 MYH15 2.69648E−25 4 128621144 128621158 INTU  2.698E−25 9 2083313 2083338 SMARCA2 3.02695E−25 20 13140617 13140637 SPTLC3 3.43592E−25 2 157370018 157370033 GPD2  3.5521E−25 12 133237753 133237768 POLE 3.73314E−25 4 146046123 146046135 ABCE1 3.78371E−25 2 66796098 66796109 MEIS1 4.00535E−25 15 48826427 48826440 FBN1 4.42733E−25 2 99936265 99936280 TXNDC9 4.60387E−25 16 70595514 70595525 SF3B3 4.61027E−25 1 65138787 65138801 CACHD1 4.85138E−25 5 78936847 78936860 PAPD4  5.1291E−25 6 32166160 32166174 NOTCH4 5.16035E−25 4 89711690 89711718 FAM13A 5.31308E−25 10 33496676 33496688 NRP1 5.47626E−25 16 4873743 4873761 GLYR1 5.51924E−25 3 97605460 97605472 CRYBG3 5.65216E−25 4 47746602 47746616 CORIN 5.72865E−25 16 15159022 15159039 PDXDC1, RRN3 5.76272E−25 1 165712555 165712571 TMCO1 5.82979E−25 5 145647187 145647210 RBM27  6.1352E−25 7 95775848 95775863 SLC25A13 6.17853E−25 7 100843369 100843385 MOGAT3 6.35445E−25 3 100438778 100438810 TFG 6.56508E−25 5 134015250 134015288 SEC24A 6.63113E−25 3 113655096 113655108 GRAMD1C 6.90378E−25 5 118576096 118576110 DMXL1 7.21041E−25 18 24039893 24039904 KCTD1  8.0175E−25 1 12368705 12368721 VPS13D 8.11113E−25 2 55883509 55883523 PNPT1 8.61191E−25 17 39776817 39776829 KRT17 8.64429E−25 12 122017848 122017866 KDM2B 8.66157E−25 6 99817699 99817713 COQ3 8.76368E−25 19 43919911 43919926 TEX101 9.24754E−25 11 56216401 56216413 OR5R1(dist = 30693), OR5M9(dist = 13532) 9.62753E−25 9 134049353 134049366 NUP214  9.7287E−25 11 102080325 102080341 YAP1 9.74675E−25 13 25899091 25899108 NUPL1 1.01972E−24 6 44364261 44364277 CDC5L  1.1359E−24 2 230656987 230657001 TRIP12 1.19674E−24 1 113657018 113657033 LRIG2 1.19724E−24 11 57094842 57094869 SSRP1 1.20319E−24 17 1584377 1584390 PRPF8 1.32252E−24 9 21861902 21861914 MTAP 1.36108E−24 3 132173004 132173026 DNAJC13 1.37153E−24 1 113159364 113159384 ST7L 1.45017E−24 4 89352469 89352487 HERC6 1.45824E−24 17 74286032 74286047 QRICH2 1.45824E−24 2 200800572 200800585 TYW5 1.47009E−24 X 19380975 19380993 MAP3K15 1.52333E−24 17 33288433 33288445 CCT6B(NM_001193530: c.-21_-33del0, 1.53997E−24 NM_001193529: c.-21_-33del0, NM_006584: c.-21_-33del0) 2 27659821 27659845 NRBP1 1.53997E−24 9 34343033 34343047 NUDT2 1.58732E−24 12 56872770 56872791 GLS2 1.62654E−24 15 51017381 51017393 SPPL2A 1.64404E−24 3 101575877 101575895 NFKBIZ 1.66704E−24 10 98336613 98336626 TM9SF3 1.66776E−24 7 98649755 98649771 SMURF1 1.72464E−24 2 27597190 27597204 SNX17 1.86401E−24 10 112360315 112360333 SMC3 1.89468E−24 14 57101560 57101576 TMEM260  1.9325E−24 7 73666736 73666750 RFC2 1.94512E−24 21 37706065 37706077 MORC3 2.00629E−24 9 27062802 27062816 IFT74(NM_001099223: c.*68_*82del0, 2.03369E−24 NM_001099222: c.*68_*82del0, NM_025103: c.*68_*82del0) 4 39233719 39233734 MIR1273H 2.04583E−24 11 16117684 16117698 SOX6 2.05894E−24 1 169586220 169586233 SELP 2.14713E−24 8 100160282 100160300 VPS13B 2.32602E−24 2 9558905 9558924 ITGB1BP1  2.4205E−24 19 10090461 10090482 COL5A3 2.51013E−24 3 130733046 130733058 ASTE1 2.53778E−24 15 66794298 66794311 RPL4 2.71306E−24 10 25140413 25140425 PRTFDC1  2.7448E−24 6 117026217 117026229 KPNA5 2.91421E−24 1 231396485 231396509 GNPAT 3.14115E−24 4 41015553 41015566 APBB2 3.23648E−24 17 29325662 29325674 RNF135 3.27565E−24 6 126249747 126249771 NCOA7 3.36146E−24 2 11332238 11332250 ROCK2 3.44599E−24 12 56504143 56504159 PA2G4 3.48105E−24 20 46282112 46282135 NCOA3 3.51773E−24 22 41551231 41551249 EP300 3.62396E−24 5 72185591 72185607 TNPO1 3.63236E−24 20 33225781 33225808 PIGU 3.64795E−24 8 22138812 22138831 PIWIL2 3.78516E−24 7 64275470 64275486 ZNF138  3.9129E−24 12 102131090 102131108 SYCP3 3.95456E−24 1 221875661 221875686 DUSP10(NM_007207: c.*93_*68del0) 3.95797E−24 5 88018369 88018402 MEF2C(NM_001193350: c.*52_*19del0, 4.12511E−24 NM_001131005: c.*52_*19del0, NM_002397: c.*52_*19del0, NM_001193347: c.*52_*19del0, NM_001193348: c.*52_*19del0, NM_001193349: c.*52_*19del0) 4 39511530 39511543 MIR1273H 4.20591E−24 9 112184972 112184987 PTPN3 4.25595E−24 5 52358761 52358775 ITGA2  4.3129E−24 14 39594134 39594146 GEMIN2 4.36485E−24 7 75185990 75186002 HIP1 4.45645E−24 8 42761288 42761308 HOOK3 4.84565E−24 14 95571635 95571647 DICER1 5.13886E−24 12 91372042 91372059 EPYC  5.5091E−24 6 152539326 152539345 SYNE1 5.55656E−24 12 120741303 120741326 SIRT4 5.77498E−24 3 160955882 160955898 NMD3 5.96846E−24 11 113697927 113697939 USP28 6.04939E−24 8 68139326 68139338 ARFGEF1 6.06739E−24 1 112303077 112303090 DDX20 6.14144E−24 20 31954819 31954834 CDK5RAP1 6.15828E−24 15 37391752 37391765 MEIS2(NM_170677: c.-85_-98del0, 6.84041E−24 NM_170676: c.-85_-98del0, NM_170675: c.-85_-98del0, NM_170674: c.-85_-98del0, NM_001220482: c.-85_-98del0) 2 21226218 21226230 APOB 6.85236E−24 20 30818497 30818514 POFUT1 7.99199E−24 8 110535444 110535460 PKHD1L1 8.01314E−24 12 31820564 31820578 METTL20 8.09202E−24 2 99788147 99788158 MITD1 8.11916E−24 10 69716602 69716614 HERC4 8.59792E−24 X 48136515 48136526 SSX1(dist = 9636), SSX9(dist = 24459) 8.89604E−24 9 100997485 100997498 TBC1D2 8.95696E−24 3 169992958 169992994 PRKC1 9.31808E−24 7 91714092 91714106 AKAP9 9.39861E−24 16 47399670 47399687 ITFG1 9.40393E−24 6 80910611 80910635 BCKDHB 9.57803E−24 14 53513439 53513452 DDHD1(NM_001160148: c.*47_*34del0, 9.92846E−24 NM_001160147: c.*47_*34del0, NM_030637: c.*47_*34del0) 4 187627659 187627676 FATI 1.06146E−23 5 67576330 67576346 PIK3R1 1.07434E−23 8 109462215 109462229 EMC2 1.08462E−23 8 134125650 134125662 TG 1.09878E−23 17 1383742 1383781 MYO1C 1.13446E−23 10 70962143 70962162 SUPV3L1 1.14778E−23 21 42823193 42823206 MX1 1.20656E−23 2 234916771 234916787 TRPM8 1.21066E−23 2 64210968 64210991 VPS54 1.24098E−23 19 34302673 34302689 KCTD15 1.30787E−23 14 73079138 73079150 RGS6(dist = 45900), DPF3(dist = 6854) 1.37113E−23 10 32327037 32327053 KIF5B 1.42745E−23 7 100319680 100319696 EPO 1.50698E−23 21 32597972 32597988 TIAM1 1.53271E−23 19 11411997 11412010 TSPAN16 1.53859E−23 X 153994469 153994482 DKC1 1.55988E−23 1 79383748 79383762 ELTD1 1.58931E−23 14 91639611 91639627 C14orf159 1.64087E−23 21 37760118 37760134 CHAF1B 1.68287E−23 6 62611334 62611348 KHDRBS2 1.68424E−23 15 43430749 43430765 TMEM62 1.73149E−23 15 102287989 102288000 TARSL2(dist = 23344), OR4F6(dist = 57923) 1.80266E−23 16 3433714 3433726 ZSCAN32  1.8428E−23 1 35885037 35885058 ZMYM4 1.84817E−23 1 166962119 166962131 MAEL 1.89614E−23 14 45587186 45587199 FKBP3 1.91118E−23 11 93490699 93490715 C11orf54  1.9662E−23 3 3216976 3216988 CRBN 1.98768E−23 13 23808732 23808745 SGCG 2.00592E−23 8 30969355 30969369 WRN 2.04194E−23 2 54146387 54146400 PSME4 2.15025E−23 21 46602483 46602497 ADARB1 2.16195E−23 14 104465128 104465144 TDRD9 2.24287E−23 3 37176656 37176670 LRRFIP2 2.29731E−23 2 209195472 209195485 PIKFYVE  2.3001E−23 3 164905648 164905660 SLITRK3(NM_014926: c.*37_*25del0) 2.31667E−23 14 81953889 81953901 SEL1L 2.42696E−23 1 114186351 114186362 MAGI3 2.56246E−23 12 51752085 51752103 GALNT6  2.5733E−23

TABLE 8 Microsatellite Repeat Marker Sequences for Brain Lower Grade Glioma (LGG). TABLE 8 - LGG ch start_pos end_pos LGG (hg37) (hg37) (hg37) gene p-value 3 5249962 5249976 EDEM1 0.003690037 9 127765856 127765868 SCAI 0.003759398 1 166962119 166962131 MAEL 0.003891051 10 17110577 17110588 CUBN 0.00390625 7 137076100 137076123 DGKI 0.00390625 1 145456732 145456747 NBPF10, NBPF20, POLR3GL 0.003952569 3 52696310 52696322 PBRM1 0.003984064 1 57349140 57349151 C8A 0.004016064 2 70463334 70463348 TIA1 0.004032258 9 130116724 130116736 GARNL3 0.004065041 8 30569609 30569622 GSR 0.004081633 5 128990138 128990150 ADAMTS19 0.004081633 10 16824085 16824108 RSU1 0.004115226 14 58471378 58471390 C14orf37(NM_001001872: c.*76_*64del0) 0.004132231 12 54920288 54920301 NCKAP1L 0.0041841 1 22030115 22030132 USP48 0.004219409 8 97245316 97245361 UOCRB 0.004219409 9 2088640 2088651 SMARCA2 0.004255319 1 176012466 176012478 RFWD2 0.004291845 8 141293914 141293943 TRAPPC9 0.004310345 7 33217071 33217084 BBS9 0.004310345 5 132408905 132408918 HSPA4 0.004329004 15 65412325 65412337 PDCD7 0.004329004 19 7995974 7996007 TIMM44 0.004347826 9 125827752 125827764 RABGAP1 0.004347826 12 58361014 58361034 XRCC6BP1(dist = 9962), LOC101927653(dist = 598708) 0.004347826 9 123922400 123922412 CNTRL 0.004405286 8 54742095 54742107 ATP6V1H 0.004424779 15 89533168 89533181 MFGE8(dist = 76505), ABHD2(dist = 98200) 0.004424779 14 76173952 76173964 TTLL5 0.004424779 X 12516777 12516790 FRMPD4 0.004444444 10 81667391 81667414 LOC100288974 0.004504505 22 29682873 29682894 EWSR1 0.004524887 5 80460576 80460591 FAH 0.004545455 2 220040216 220040231 CNPPD1 0.004545455 14 50760968 50760980 L2HGDH 0.004587156 2 201534173 201534187 AOX1 0.004587156 4 17841869 17841881 NCAPG 0.004587156 9 131721441 131721453 NUP188 0.004587156 2 183960133 183960155 DUSP19 0.00462963 7 131113756 131113779 MKLN1 0.00462963 21 27136460 27136473 GABPA 0.00462963 5 72185591 72185607 TNPO1 0.00462963 7 104707158 104707171 KMT2E 0.004651163 6 7402813 7402824 RIOK1 0.004672897 9 19328009 19328021 DENND4C 0.004694836 8 1844623 1844634 ARHGEF10 0.004694836 3 9730522 9730543 MTMR14 0.004694836 5 159841492 159841507 SLU7 0.004716981 2 15676703 15676717 NBAS 0.004739336 13 77644856 77644877 MYCBP2 0.004739336 2 114210810 114210837 CBWD2 0.004739336 11 60182851 60182862 MS4A14 0.004761905 9 19350679 19350691 DENND4C 0.004784689 1 89614950 89614962 GBP7 0.004807692 11 134055425 134055436 NCAPD3 0.004807692 7 65426054 65426069 GUSB 0.004830918 1 71535064 71535075 ZRANB2 0.004830918 20 3565277 3565289 ATRN 0.004854369 1 117633133 117633144 TTF2 0.004854369 4 13371622 13371645 RAB28 0.004854369 5 145508515 145508535 LARS 0.004926108 1 235621851 235621865 B3GALNT2 0.004950495 1 220355521 220355533 RAB3GAP2 0.004950495 6 55739711 55739726 BMP5(NM_021073: c.-48_-63del0) 0.005 14 39594134 39594146 GEMIN2 0.005050505 6 166831580 166831594 RPS6KA2 0.005076142 16 71682686 71682711 PHLPP2(NM_015020: c.*107_*82del0, 0.005102041 NM_001289003: c.*107_*82del0) 8 38940143 38940157 ADAM9 0.005128205 14 75508258 75508303 MLH3 0.005263158 4 56277766 56277777 TMEM165 0.005376344 20 43623620 43623658 STK4 0.005464481 1 45976928 45976939 PRDX1(NM_001202431: c.*73_*62del0, 0.005464481 NM_002574: c.*73_*62del0, NM_181697: c.*73_*62del0, NM_181696: c.*73_*62del0) 11 28113094 28113107 KIF18A 0.005494505 6 137193301 137193332 PEX7 0.005494505 7 33192288 33192300 BBS9 0.005555556 15 42503953 42503965 TMEM87A 0.005555556 6 155109168 155109189 SCAF8 0.005555556 12 110924566 110924578 FAM216A 0.005586592 14 73079138 73079150 RGS6(dist = 45900), DPF3(dist = 6854) 0.005780347 11 58385231 58385251 ZFP91-CNTF 0.005952381 5 180482303 180482317 BTNL9 0.005988024 1 223156384 223156419 DISP1 0.005988024 8 124822507 124822519 FAM91A1 0.006060606 3 196792356 196792367 DLG1 0.006097561 19 16613797 16613832 C19orf44 0.00617284 2 209110161 209110186 IDH1 0.006289308 8 28989764 28989782 KIF13B 0.006756757 19 18857939 18857956 CRTC1 0.006993007 7 106523362 106523383 PIK3CG 0.007067138 2 166898938 166898948 SCN1A 0.007194245 17 29528313 29528336 NF1 0.007246377 2 10269544 10269555 RRM2(NM_001165931: c.*31_*42del0, 0.007407407 NM_001034: c.*31_*42del0) 12 133237753 133237768 POLE 0.007575758 12 122437594 122437605 WDR66 0.007692308 3 50095096 50095119 RBM6 0.007751938 18 14218568 14218580 ANKRD20A5P 0.008097166 6 15651642 15651656 DTNBP1 0.008130081 14 62261603 62261633 SNAPC1 0.008163265 2 201950159 201950178 NDUFB3 0.008264463 1 112303077 112303090 DDX20 0.008298755 8 130874614 130874639 FAM49B 0.008298755 21 37787572 37787585 CHAF1B 0.008298755 22 38766061 38766082 LOC400927 0.008583691 7 134626034 134626049 CALD1 0.00862069 14 104145625 104145642 KLC1 0.00862069 11 122817187 122817199 C11orf63 0.008658009 8 62550924 62550938 ASPH 0.008658009 7 92883250 92883261 CCDC132 0.008695652 9 75420448 75420463 TMC1 0.008733624 2 64069277 64069293 UGP2(NM_006759: c.-43_-27del-) 0.008733624 18 9279678 9279703 ANKRD12 0.008733624 15 73418741 73418756 NEO1 0.008849558 7 150269192 150269204 GIMAP4 0.008849558 17 46248074 46248089 SKAP1 0.008849558 20 60861505 60861519 OSBPL2 0.008888889 8 38839302 38839316 HTRA4 0.00896861 12 25678995 25679008 LMNTD1 0.00896861 7 152055766 152055780 KMT2C 0.00896861 4 123109034 123109048 KIAA1109 0.009009009 1 70742532 70742545 ANKRD13C 0.009009009 2 32427092 32427104 SLC30A6 0.009389671 1 78432506 78432521 FUBP1 0.009389671 20 47648454 47648481 ARFGEF2 0.009478673 2 102785158 102785171 IL1R1 0.009478673 4 41015553 41015566 APBB2 0.00952381 2 239241445 239241460 TRAF3IP1 0.009615385 12 53861636 53861650 PCBP2 0.009661836 5 58270446 58270485 PDE4D(NM_001197223: c.*45_*6del0, 0.009756098 NM_001197221: c.*45_*6del0, NM_001197220: c.*45_*6del0, NM_001165899: c.*45_*6del0, NM_001197218: c.*45_*6del0, NM_001197222: c.*45_*6del0, NM_001197219: c.*45_*6del0, NM_006203: c.*45_*6del0, NM_001104631: c.*45_*6del0) 3 127820493 127820505 RUVBL1 0.009803922 17 49048274 49048312 SPAG9 0.009803922 17 47076449 47076462 IGF2BP1 0.009803922 12 53470811 53470838 SPRYD3 0.00990099 19 47656338 47656359 SAE1 0.01 15 41770598 41770624 RTF1 0.01010101 6 88853530 88853542 CNR1(NM_001160259: c.*45_*33del0, 0.010204082 NM_001160226: c.*45_*33del0, NM_001160258: c.*45_*33del0, NM_033181: c.*45_*33del0, NM_016083: c.*45_*33del0) 11 14316128 14316148 RRAS2 0.010204082 19 12112120 12112142 ZNF763(dist = 20922), ZNF433(dist = 13390) 0.010416667 17 74625858 74625883 ST6GALNAC1 0.010416667 6 149899943 149899954 GINM1 0.010752688 8 194596 194607 ZNF596 0.010752688 10 94694025 94694037 EXOC6 0.010810811 5 108168451 108168468 FER 0.010810811 19 34302673 34302689 KCTD15 0.010909091 1 149900985 149901002 MTMR11(NM_001145862: c.*36_*19del0) 0.010948905 10 75576885 75576896 CAMK2G 0.010989011 16 10851655 10851666 NUBP1 0.011173184 8 68140383 68140394 ARFGEF1 0.011235955 12 55820958 55820971 OR6C76 0.011235955 6 32147291 32147312 RNF5P1 0.011428571 1 74575199 74575231 LRRIQ3 0.011695906 12 99059316 99059327 APAF1 0.012048193 7 73279233 73279260 WBSCR28 0.012121212 6 70040500 70040513 BAI3 0.012195122 11 74790486 74790510 NEU3(dist = 71743), OR2AT4(dist = 9286) 0.012269939 2 27708007 27708031 IFT172 0.012396694 10 69716602 69716614 HERC4 0.012448133 16 67470052 67470095 HSD11B2 0.0125 17 10317164 10317176 MYHAS 0.0125 19 10090461 10090482 COL5A3 0.0125 16 19063220 19063235 TMC7 0.012658228 4 141448595 141448610 ELMOD2 0.012711864 13 73293238 73293264 MZT1 0.012765957 12 122966016 122966028 ZCCHC8 0.012987013 3 195022926 195022944 ACAP2 0.013043478 6 160157277 160157288 WTAP 0.013215859 20 4850568 4850578 SLC23A2 0.013245033 1 14057425 14057439 PRDM2 0.013274336 20 10622080 10622091 JAG1 0.013513514 1 168200730 168200743 SFT2D2 0.013513514 2 179595571 179595589 TTN 0.013888889 17 57937792 57937807 TUBD1 0.013953488 1 180757007 180757018 XPR1 0.013953488 11 55656437 55656451 TRIM51 0.014218009 6 117753497 117753511 ROS1(dist = 6479), DCBLD1(dist = 50309) 0.014218009 17 29563068 29563089 NF1 0.014285714 1 213180434 213180459 ANGEL2 0.014336918 1 19683355 19683368 CAPZB 0.014354067 12 89995053 89995065 ATP2B1 0.014492754 5 36629801 36629815 SLC1A3 0.014492754 3 195956726 195956749 SLC51A 0.014563107 16 75670529 75670550 KARS 0.014705882 1 193038176 193038186 TROVE2 0.014814815 18 56279052 56279066 ALPK2 0.015075377 19 37967219 37967230 ZNF570 0.015075377 11 108014684 108014704 ACAT1 0.015075377 5 96116095 96116125 ERAP1 0.015151515 12 21958998 21959011 ABCC9 0.015564202 15 55789793 55789806 DYX1C1-CCPG1 0.015625 4 47163234 47163248 GABRB1 0.015748031 12 16713487 16713501 LMO3 0.016129032 12 27841925 27841938 PPFIBP1 0.016194332 4 114176848 114176860 ANK2 0.016460905 14 69861462 69861490 ERH 0.016666667 4 156725681 156725695 GUCY1B3 0.016666667 1 46726867 46726890 RAD54L 0.016759777 7 40087320 40087333 CDK13 0.016853933 12 53823175 53823189 AMHR2 0.016877637 3 77645936 77645960 ROBO2 0.016877637 2 167138320 167138331 SCN9A 0.016949153 5 169020337 169020350 SPDL1 0.016949153 19 41188890 41188901 NUMBL 0.017142857 15 58891938 58891962 ADAM10 0.017241379 16 50368677 50368692 BRD7 0.017241379 2 158283943 158283954 CYTIP 0.017241379 6 24412431 24412445 MRS2 0.017467249 1 173795803 173795821 DARS2 0.017699115 10 12240681 12240702 CDC123 0.01793722 8 95507237 95507250 KIAA1429 0.018348624 X 36156447 36156461 CHDC2 0.018518519 15 31220709 31220744 FAN1 0.019323671 9 135133867 135133881 NTNG2(dist = 15647), SETX(dist = 2946) 0.019607843 17 16344523 16344534 LRRC75A-AS1 0.019736842 17 18708830 18708843 TVP23B 0.01980198 5 147785802 147785816 FBXO38 0.02 2 56102061 56102072 EFEMP1 0.020134228 13 42772765 42772789 DGKH 0.020304569 12 94575162 94575177 PLXNC1 0.020547945 1 92765880 92765892 RPAP2 0.020833333 12 56500502 56500515 PA2G4 0.021052632 15 49097732 49097750 CEP152 0.021126761 7 81641570 81641584 LOC101927356 0.021551724 7 126086436 126086447 GRM8 0.021621622 3 148858987 148859001 HPS3 0.02173913 13 111340025 111340053 CARS2 0.022058824 11 33374613 33374626 HIPK3 0.022222222 1 201754396 201754428 IPO9-AS1, RNU6-79P 0.02247191 20 50781298 50781310 ZFP64 0.022727273 5 67576330 67576346 PIK3R1 0.022857143 4 146031236 146031253 ABCE1 0.022988506 17 6662948 6662977 XAF1 0.023121387 16 15133783 15133795 NTAN1, PDXDC1 0.023696682 4 7817686 7817710 AFAP1 0.023696682 6 102124470 102124483 GRIK2 0.024 11 93454831 93454868 SCARNA9 0.024242424 6 49415351 49415368 MUT 0.025641026 5 137513369 137513382 BRD8 0.02617801 10 116735234 116735260 TRUB1(NM_139169: c.*96_*122del0) 0.026315789 1 70904523 70904552 CTH 0.026737968 19 37155495 37155509 ZNF461 0.027027027 21 30925853 30925869 GRIK1(NM_000830: c.*10_*7del0) 0.029166667 14 93686568 93686587 UBR7 0.029288703 16 4700318 4700337 MGRN1 0.03 4 3040279 3040293 GRK4 0.03030303 8 75944409 75944422 CRISPLD1 0.031674208 6 90366329 90366347 LOC101929057 0.03187251 3 122271204 122271215 PARP9 0.031914894 12 76763092 76763106 OSBPL8 0.033057851 1 236744720 236744735 HEATRI 0.033613445 67165932 67165942 PPPICA(NM_002708: c._*74_*64del0, 0.034090909 NM_206873: c._*74_*64del0, NM_001008709: c.*74_*64del0) 1 114092111 114092124 MAGI3 0.034188034 14 55429897 55429917 WDHD1 0.034482759 6 151859146 151859161 CCDC170 0.035175879 1 245021291 245021305 HNRNPU 0.035353535 15 42111745 42111756 MAPKBP1 0.035460993 6 52400479 52400497 TRAM2 0.038961039 4 122590883 122590899 ANXA5 0.039525692 2 183806893 183806904 NCKAP1 0.040983607 9 2097548 2097560 SMARCA2 0.042424242 19 41703604 41703616 CYP2S1 0.042780749 12 109701959 109701975 ACACB 0.042857143 6 167453519 167453532 FGFR1OP(NM_007045: c.*53_*66del0, 0.043478261 NM_194429: c.*53_*66del0) 13 50306823 50306836 KPNA3 0.043478261 10 5788110 5788126 FAM208B 0.04845815 1 67154730 67154748 SGIP1 0.048672566 10 71647196 71647209 COL13A1 0.049586777

TABLE 9 Microsatellite Repeat Marker Sequences for Prostate Adenocarcinoma (PRAD). TABLE 9 - PRAD ch start_pos end_pos PRAD (hg37) (hg37) (hg37) gene p-value 1 150932953 150932989 SETDB1 3.48675E−05 19 14104688 14104703 RFX1(NM_002918: c.-33_-48del0)  3.6062E−05 8 42761288 42761308 HOOK3 3.96825E−05 3 180320897 180320910 TTC14 4.07647E−05 4 26417055 26417080 RBPJ  4.3877E−05 5 94842718 94842730 TTC37 4.64511E−05 2 66796098 66796109 MEIS1 4.69021E−05 1 202736222 202736233 KDM5B 4.69021E−05 1 151380720 151380737 POGZ 4.69021E−05 3 164905648 164905660 SLITRK3(NM_014926: c.*37_*25del0) 4.97512E−05 22 32482127 32482141 SLC5A1 5.02513E−05 10 115380483 115380497 NRAP 5.12742E−05 22 31942815 31942840 SFI1 5.45375E−05 10 27037487 27037499 ABI1 6.20732E−05 10 122630877 122630889 MIR5694  6.348E−05 2 8998775 8998788 MBOAT2(NM_138799: c.*34_*21del0) 6.56814E−05 1 161829973 161829987 ATF6 6.64408E−05 6 32147291 32147312 RNF5P1 6.96136E−05 20 54823684 54823699 MC3R 7.21449E−05 13 37596114 37596125 SUPT20H 7.57404E−05 11 117152291 117152314 RNF214  8.2713E−05 5 178140630 178140648 ZNF354A  9.3188E−05 11 32610726 32610740 EIF3M 0.000106372 22 35719378 35719394 TOM1 0.000111957 8 95186510 95186526 CDH17 0.000111957 6 111329221 111329239 RPF2 0.000114916 14 73079138 73079150 RGS6(dist = 45900), DPF3(dist = 6854) 0.00011566 6 13316780 13316795 TBC1D7 0.000120115 8 101933023 101933037 YWHAZ 0.000123031 20 2474136 2474149 ZNF343 0.000123406 18 649879 649895 TYMSOS(NM_001012716: c.*120_*104del0) 0.000126834 2 60988862 60988872 PAPOLG 0.000129032 20 30818497 30818514 POFUT1 0.000129199 14 58471378 58471390 C14orf37(NM_001001872: c.*76_*64del0) 0.000130406 1 84956161 84956173 RPF1 0.000140706 21 37706065 37706077 MORC3 0.000143472 2 86998651 86998676 RMND5A 0.000147776 13 111340025 111340053 CARS2 0.000155255 12 48360947 48360961 TMEM106C 0.000192604 12 31820564 31820578 METTL20 0.000194805 4 47163234 47163248 GABRB1 0.000205754 15 83808031 83808046 HDGFRP3 0.000210963 15 42503953 42503965 TMEM87A 0.000216435 5 67576330 67576346 PIK3R1 0.000227221 15 41770639 41770652 RTF1 0.000242395 8 141293914 141293943 TRAPPC9 0.000242395 1 151384052 151384067 POGZ 0.000258398 6 31832356 31832372 SLC44A4 0.000268264 2 201534173 201534187 AOX1 0.000278707 9 163927 163943 CBWD1 0.000279564 13 28133956 28133972 LNX2 0.000295552 12 8692327 8692338 CLEC4E 0.000320496 7 94989255 94989273 PON3(NM_000940: c.*30_*12del0) 0.000323834 2 183841691 183841704 NCKAP1 0.000333 17 8417006 8417020 MYH10 0.000345006 20 55206241 55206253 TFAP2C 0.000432869 16 4873743 4873761 GLYR1 0.000448954 5 78416973 78416990 BHMT 0.00049373 9 77550305 77550323 TRPM6(dist = 47295), C9orf40(dist = 11176) 0.000589971 8 23712066 23712089 STC1(NM_003155: c.-30_-53del0) 0.000606061 11 65268479 65268492 MALAT1 0.000613874 14 74534274 74534284 ALDH6A1 0.000657895 8 17422434 17422446 SLC7A2 0.000686342 17 80443296 80443308 NARF 0.000910692 7 92129161 92129183 PEX1 0.001057865 1 67154730 67154748 SGIP1 0.001326072 5 70809269 70809285 BDP1 0.001407035 16 15133783 15133795 NTAN1, PDXDC1 0.001559454 4 52928352 52928371 SPATA18 0.002125357 10 94366347 94366370 KIF11 0.003623188 8 100287517 100287536 VPS13B 0.003921569 7 114303617 114303633 FOXP2 0.004101162 1 24857651 24857670 RCAN3 0.004219409 12 21958998 21959011 ABCC9 0.004310345 14 21702046 21702071 HNRNPC 0.004310345 3 52696310 52696322 PBRM1 0.004347826 8 95777578 95777591 DPY19L4 0.004347826 21 30433900 30433919 CCT8 0.004347826 10 26998490 26998502 PDSS1 0.004347826 19 6026288 6026302 RFX2 0.004464286 3 113655096 113655108 GRAMD1C 0.004464286 12 133237753 133237768 POLE 0.004484305 8 104054513 104054532 ATP6V1C1 0.004484305 2 157370018 157370033 GPD2 0.004504505 4 47886322 47886342 LOC101927179 0.004524887 19 4292947 4292975 TMIGD2 0.004524887 6 46636556 46636581 SLC25A27 0.004545455 9 98703711 98703723 ERCC6L2 0.004545455 3 172052897 172052914 FNDC3B 0.00456621 1 173795803 173795821 DARS2 0.00456621 17 1584377 1584390 PRPF8 0.00456621 2 32117217 32117230 MEMO1 0.004587156 2 192011485 192011497 STAT4 0.004608295 11 107904512 107904524 CUL5 0.004608295 8 71037103 71037115 NCOA2 0.004672897 7 131113756 131113779 MKLN1 0.004672897 X 18183097 18183113 BEND2(NM_153346: c.*32_*16del0) 0.004672897 X 153994469 153994482 DKC1 0.004694836 2 48688258 48688273 PPP1R21 0.004694836 22 26899774 26899785 TFIP11 0.004694836 X 113965679 113965691 HTR2C 0.004694836 17 39776817 39776829 KRT17 0.004761905 4 57897508 57897530 IGFBP7 0.004784689 6 42559866 42559879 UBR2 0.004830918 13 103301601 103301612 TPP2 0.004830918 10 112649255 112649287 PDCD4 0.004854369 3 97605460 97605472 CRYBG3 0.004901961 4 89352469 89352487 HERC6 0.004950495 22 29879265 29879302 NEFH 0.004975124 7 5239305 5239336 WIPI2 0.005 3 113169372 113169386 SPICE1 0.005025126 7 131130509 131130538 MKLN1 0.005025126 13 99890849 99890862 MIR548AN 0.005076142 6 117026217 117026229 KPNA5 0.005076142 17 18785823 18785842 PRPSAP2 0.005076142 6 128330423 128330435 PTPRK 0.005128205 8 74495112 74495130 STAU2 0.005128205 14 103915242 103915254 MARK3 0.005181347 10 88834244 88834265 GLUD1 0.005181347 3 100992404 100992415 IMPG2 0.005181347 3 100438778 100438810 TFG 0.005208333 20 4839890 4839911 SLC23A2 0.005263158 6 163235158 163235170 PACRG 0.005263158 21 33068865 33068877 SCAF4 0.005263158 2 54146387 54146400 PSME4 0.005291005 17 4880231 4880257 CAMTA2 0.005291005 6 96971185 96971208 UFL1 0.005319149 15 55841195 55841209 PYGO1 0.005347594 5 129070812 129070838 ADAMTS19 0.005347594 7 74608740 74608754 GTF2IP1, LOC100093631 0.005376344 9 97555228 97555242 C9orf3 0.005376344 9 2083313 2083338 SMARCA2 0.005376344 11 59836986 59836998 MS4A3 0.005405405 16 15138162 15138182 NTAN1, PDXDC1 0.005405405 5 137763868 137763912 KDM3B 0.005405405 11 73753268 73753288 C2CD3 0.005434783 3 170715672 170715694 SLC2A2 0.005464481 9 33886999 33887011 UBE2R2 0.005524862 3 24270412 24270424 THRB 0.005524862 6 166831580 166831594 RPS6KA2 0.005524862 10 75576885 75576896 CAMK2G 0.005555556 4 56770490 56770501 EXOC1 0.005586592 15 59961570 59961607 BNIP2 0.005617978 2 32427092 32427104 SLC30A6 0.005649718 6 163899794 163899807 QKI 0.005681818 20 46266543 46266558 NCOA3 0.005714286 21 42838093 42838104 TMPRSS2 0.005714286 2 222290623 222290635 EPHA4(NM_004438: c.*125_*113del0) 0.005747126 5 37326073 37326084 NUP 155 0.005747126 3 44815871 44815883 KIF15 0.005780347 11 110306734 110306760 FDX1 0.005813953 18 31523144 31523156 NOL4 0.005813953 1 115276971 115276990 CSDE1 0.005844535 2 238632159 238632170 LRRFIP1 0.005847953 17 26653806 26653817 TMEM97 0.005847953 19 7670033 7670064 CAMSAP3 0.005847953 20 60711773 60711796 PSMA7(NM_002792: c.*130_*117del0) 0.005882353 2 175246545 175246557 CIR1 0.005952381 15 57545438 57545449 TCF12 0.006060606 16 5129689 5129703 ALG1 0.006097561 6 49459994 49460005 CENPQ(NM_018132: c.*6_*17del0) 0.006097561 15 70961809 70961821 UACA 0.006097561 14 73465027 73465043 ZFYVE1 0.006097561 2 61622374 61622387 USP34 0.006134969 3 47604262 47604281 CSPG5 0.006134969 5 150856066 150856091 SLC36A1 0.00617284 1 99164246 99164260 SNX7 0.00625 6 20758808 20758822 CDKAL1 0.006289308 15 35149313 35149327 AQR 0.006289308 15 41364265 41364305 INO80 0.006329114 1 225607366 225607387 LBR 0.006329114 3 141622616 141622641 ATP1B3 0.006329114 3 52728303 52728323 GNL3(NM_014366: c.*12_*32del0, 0.006369427 NM_206825: c.*12_*32del0, NM_206826: c.*12_*32del0) 2 165365365 165365376 GRB14 0.006410256 6 80837242 80837253 BCKDHB 0.006410256 10 121678931 121678952 SEC23IP 0.006410256 2 103281540 103281552 SLC9A2 0.006451613 8 68140383 68140394 ARFGEF1 0.006493506 4 71693494 71693508 GRSF1 0.006493506 19 9528423 9528438 ZNF266 0.006493506 7 23823176 23823194 STK31 0.006535948 2 64210968 64210991 VPS54 0.006578947 11 89502007 89502036 TRIM77(dist = 50967), TRIM49(dist = 28787) 0.006578947 12 104515109 104515121 NFYB 0.006666667 13 39603371 39603407 PROSER1 0.006666667 17 35979746 35979761 DDX52 0.006711409 1 41456808 41456823 CTPS1 0.006802721 17 7306338 7306349 TMEM256-PLSCR3 0.006802721 3 154007618 154007629 DHX36 0.006802721 4 184567431 184567444 RWDD4 0.006802721 20 3928832 3928855 RNF24 0.006896552 X 135328309 135328320 MAP7D3 0.007092199 16 29110397 29110417 RRN3P2 0.007092199 1 1688823 1688845 NADK 0.007142857 12 69107631 69107642 NUP107 0.007194245 5 72168575 72168596 TNPO1 0.007352941 14 64496810 64496822 MIR548AZ 0.007352941 14 92562967 92562986 ATXN3 0.007352941 18 30913142 30913153 CCDC178 0.007407407 17 73515055 73515068 TSEN54 0.007462687 7 44663890 44663910 OGDH 0.007462687 18 63430040 63430078 CDH7(NM_033646: c.-39_-1del-, 0.007462687 NM_004361: c.-39_-1del-) 5 134007593 134007616 SEC24A 0.007462687 5 143853686 143853711 KCTD16(NM_020768: c.*9_*34del0) 0.007518797 17 7700419 7700440 DNAH2 0.007633588 16 31202698 31202716 FUS 0.007843137 17 5324558 5324611 RPAIN 0.007874016 15 59009930 59009941 ADAM10 0.007874016 14 21960425 21960451 TOX4 0.007936508 2 215821543 215821563 LOC101928103 0.007936508 2 111406968 111406984 BUB1 0.008032129 17 30190540 30190551 UTP6 0.008064516 15 86768264 86768280 AGBL1 0.008130081 4 89711690 89711718 FAM13A 0.008196721 17 5044640 5044653 USP6 0.008196721 8 27637666 27637677 ESCO2 0.008196721 17 38028508 38028519 ZPBP2 0.008196721 22 36650908 36650919 APOL1 0.008333333 4 76997157 76997173 ART3 0.008368201 17 1582787 1582825 PRPF8 0.008368201 3 50095096 50095119 RBM6 0.008368201 2 27824348 27824360 ZNF512 0.008368201 9 52625 52641 FAM138C(dist = 16761), PGM5P3-AS1(dist = 20049) 0.008403361 19 34302673 34302689 KCTD15 0.008403361 7 31132235 31132249 ADCYAP1R1 0.008403361 22 36872638 36872662 TXN2 0.008403361 2 206997835 206997847 NDUFS1 0.008403361 4 141448595 141448610 ELMOD2 0.008438819 9 36109839 36109853 RECK 0.008438819 12 54646020 54646054 CBX5 0.008474576 5 98224945 98224957 CHD1 0.008474576 3 57850505 57850518 SLMAP 0.008510638 14 57101560 57101576 TMEM260 0.008510638 16 69293926 69293945 SNTB2 0.008547009 1 220284112 220284124 RNU5F-1 0.008547009 12 59307848 59307866 LRIG3 0.008547009 1 54252939 54252952 NDC1 0.008583691 1 222904869 222904881 BROX 0.00862069 1 169845236 169845247 SCYL3 0.00862069 16 31196218 31196237 FUS 0.008658009 9 73164596 73164610 TRPM3 0.008658009 3 137892531 137892543 DBR1 0.008658009 5 78373251 78373265 BHMT2 0.008658009 14 61446607 61446626 TRMT5 0.008658009 12 4645161 4645173 C12orf4 0.008695652 1 12368705 12368721 VPS13D 0.008695652 8 134125650 134125662 TG 0.008733624 17 29508819 29508836 NF1 0.00877193 2 9558905 9558924 ITGB1BP1 0.00877193 10 26825151 26825168 APBB1IP 0.008810573 8 133984814 133984834 TG 0.008849558 7 138951165 138951177 UBN2 0.008849558 6 166578165 166578177 T 0.008849558 10 16824085 16824108 RSU1 0.008888889 5 179032860 179032871 RUFY1 0.008888889 11 108188266 108188280 ATM 0.008888889 17 10317164 10317176 MYHAS 0.008928571 7 7572355 7572381 COL28A1 0.008928571 10 112044559 112044572 MXI1 0.008928571 9 5811331 5811349 ERMP1 0.00896861 1 173490547 173490571 SLC9C2 0.00896861 1 221875661 221875686 DUSP10(NM_007207: c.*93_*68del0) 0.00896861 9 19334957 19334970 DENND4C 0.009009009 3 160960468 160960478 NMD3 0.009009009 15 52903303 52903313 FAM214A 0.009009009 10 112360315 112360333 SMC3 0.009049774 11 122817187 122817199 C11orf63 0.009049774 9 131743701 131743715 NUP188 0.009090909 9 79820192 79820224 VPS13A 0.009090909 12 56994331 56994349 BAZ2A 0.009090909 1 112958898 112958910 CTTNBP2NL 0.009090909 20 10273694 10273715 SNAP25 0.00913242 11 47187055 47187087 ARFGAP2 0.00913242 9 80343587 80343612 GNAQ 0.00913242 5 31435975 31435987 DROSHA 0.00913242 1 155747369 155747381 GON4L 0.00913242 1 115226990 115227003 AMPD1 0.009174312 10 101510104 101510123 CUTC 0.009174312 3 19498221 19498253 KCNH8 0.00921659 1 3549854 3549874 WRAP73 0.00921659 3 67058329 67058357 KBTBD8 0.00921659 15 66794298 66794311 RPL4 0.009259259 19 11411997 11412010 TSPAN16 0.009259259 7 137076100 137076123 DGKI 0.009345794 2 179407763 179407779 MIR548N, TTN-AS1 0.009345794 12 56380950 56380964 RAB5B 0.009345794 20 42265908 42265920 IFT52 0.009345794 6 111701462 111701475 REV3L 0.009345794 X 107169290 107169321 LOC101928335 0.009345794 6 80910611 80910635 BCKDHB 0.009389671 19 10090461 10090482 COL5A3 0.009389671 10 12162338 12162351 DHTKD1 0.009389671 1 70654981 70655003 LRRC40 0.009433962 2 27463091 27463105 CAD 0.009433962 12 9220823 9220847 A2M 0.009433962 19 53050992 53051013 ZNF808 0.009433962 3 33725814 33725828 CLASP2 0.009478673 5 6623405 6623418 NSUN2 0.00952381 5 94903575 94903589 ARSK 0.00952381 3 42602535 42602546 SEC22C 0.00952381 3 15613279 15613304 HACL1 0.009569378 8 107704921 107704955 OXR1 0.009615385 14 50760968 50760980 L2HGDH 0.009615385 9 114341239 114341255 PTGR1 0.009615385 12 107080617 107080640 LOC100287944 0.009615385 19 37967219 37967230 ZNF570 0.009615385 16 21138881 21138894 DNAH3 0.009615385 19 50951721 50951743 MYBPC2 0.009661836 4 151850226 151850239 LRBA 0.009708738 2 37487341 37487353 PRKD3 0.009708738 6 133093231 133093247 SLC18B1 0.009708738 2 197531518 197531530 CCDC150 0.009708738 3 142241692 142241705 ATR 0.009708738 7 6485740 6485753 DAGLB 0.009708738 2 37464877 37464888 NDUFAF7 0.009708738 3 65456181 65456211 MAGI1 0.009756098 3 62153593 62153621 PTPRG 0.009803922 3 146167163 146167186 PLSCR2 0.009803922 9 78638564 78638576 PCSK5 0.009803922 2 217329413 217329447 SMARCAL1 0.009803922 4 83970297 83970312 COPS4 0.009803922 13 39435552 39435564 FREM2 0.009803922 12 42768646 42768660 PPHLN1 0.009803922 6 42611936 42611951 UBR2 0.009852217 14 59787325 59787338 DAAM1 0.009852217 2 79314062 79314073 REG1B 0.009852217 9 33280749 33280775 CHMP5 0.009852217 11 28113094 28113107 KIF18A 0.00990099 11 134188851 134188867 GLB1L3(NM_001080407: c.*15_*31del0) 0.00990099 15 48717850 48717884 FBN1 0.009950249 7 76883792 76883819 CCDC146 0.009950249 1 204494748 204494783 MDM4 0.009950249 3 113442784 113442795 NAA50 0.01 7 135099044 135099059 CNOT4 0.01 5 179150788 179150800 CANX 0.01 17 58013510 58013529 RPS6KB1 0.01 13 50134014 50134026 RCBTB1 0.01 5 137451460 137451472 NME5 0.010050251 22 44589636 44589647 PARVG 0.010050251 15 45725103 45725138 C15orf48 0.01010101 1 11134470 11134485 EXOSC10 0.01010101 17 39976721 39976731 FKBP10 0.01010101 11 134118382 134118401 THYN1 0.01010101 1 24180806 24180833 FUCA1 0.01010101 3 51504906 51504917 VPRBP 0.01010101 16 3808052 3808066 CREBBP 0.010152284 7 123332378 123332391 WASL 0.010152284 2 102979238 102979250 IL18R1 0.010152284 5 34945797 34945810 DNAJC21 0.010152284 2 197654578 197654593 GTF3C3 0.010204082 6 90452808 90452835 MDN1 0.010204082 2 207027356 207027368 EEF1B2 0.010204082 6 25452453 25452466 LRRC16A 0.010204082 1 153949135 153949147 JTB 0.01025641 11 55656437 55656451 TRIM51 0.01025641 4 169612452 169612484 PALLD 0.01025641 16 48333493 48333512 MIR548AE2 0.01025641 20 13140617 13140637 SPTLC3 0.010309278 12 81239721 81239737 LIN7A 0.010309278 1 158298679 158298691 CD1B 0.010309278 12 31435608 31435620 FAM60A(NM_001135811: c.*38_*26del0, 0.010362694 NM_001135812: c.*38_*26del0, NM_021238: c.*38_*26del0) 21 30435646 30435668 CCT8 0.010416667 15 48826427 48826440 FBN1 0.010416667 9 98230924 98230947 LOC100507346 0.010416667 2 152424933 152424962 NEB 0.010416667 4 47746602 47746616 CORIN 0.010471204 7 75185990 75186002 HIP1 0.010471204 5 122343337 122343374 SNX24 0.010471204 2 61319728 61319740 KIAA1841 0.010471204 7 99672649 99672660 ZNF3 0.010471204 17 74286032 74286047 QRICH2 0.010526316 14 81953889 81953901 SEL1L 0.010526316 6 76618182 76618195 MY06 0.010526316 20 34430474 34430486 PHF20 0.010582011 6 137325901 137325917 IL20RA 0.010582011 1 114186351 114186362 MAGI3 0.010582011 1 155679543 155679557 DAP3 0.010582011 17 29482977 29482998 NF1 0.010582011 6 70459209 70459222 LMBRD1 0.010638298 1 186330695 186330709 MIR548F1 0.010638298 8 80831393 80831407 MRPS28 0.010638298 3 186302391 186302439 DNAJB11 0.010638298 2 172187261 172187296 METTL8 0.010638298 7 6771663 6771684 ZNF12(dist = 25097), PMS2CL(dist = 3252) 0.010638298 14 92549604 92549623 ATXN3 0.010695187 1 19683355 19683368 CAPZB 0.010695187 8 94817177 94817188 TMEM67 0.010752688 1 150799125 150799138 ARNT 0.010810811 14 31762500 31762511 HEATR5A 0.010810811 12 51323672 51323684 METTL7A 0.010869565 4 74010555 74010571 ANKRD17 0.010869565 9 75420448 75420463 TMC1 0.010928962 16 67854644 67854670 TSNAXIP1 0.010928962 9 19299209 19299224 DENND4C 0.010989011 11 119145463 119145476 CBL 0.010989011 7 63673449 63673467 ZNF735 0.010989011 12 93149720 93149731 PLEKHG7 0.010989011 X 52654536 52654550 SSX8 0.011049724 1 22030891 22030902 USP48 0.011049724 1 202407189 202407200 PPP1R12B 0.011111111 10 21901247 21901268 MLLT10 0.011111111 9 98009613 98009626 FANCC 0.011173184 3 160134195 160134221 SMC4 0.011173184 6 136429995 136430013 PDE7B 0.011173184 13 25416104 25416116 RNF17 0.011173184 2 71645619 71645662 ZNF638 0.011173184 11 3381798 3381814 ZNF195 0.011173184 16 20749284 20749296 THUMPD1 0.011235955 2 11913727 11913739 LPIN1 0.011235955 5 87494728 87494767 TMEM161B 0.011235955 13 48664556 48664569 MED4 0.011299435 2 21226218 21226230 APOB 0.011299435 5 138760853 138760870 DNAJC18 0.011299435 3 122081881 122081893 CCDC58 0.011363636 5 180482303 180482317 BTNL9 0.011428571 7 121699789 121699802 PTPRZ1 0.011494253 20 37126168 37126180 RALGAPB 0.011494253 1 210411266 210411281 SERTAD4 0.011494253 11 134064516 134064540 NCAPD3 0.011494253 7 23239063 23239074 NUPL2 0.011494253 1 89449508 89449520 RBMXL1 0.011560694 12 3935279 3935290 PARP11 0.011627907 12 53573482 53573510 CSAD 0.011627907 18 214605 214622 THOC1(NM_005131: c.*21_*4del0) 0.011627907 13 48828102 48828118 ITM2B 0.011695906 6 24589046 24589057 KIAA0319 0.011695906 16 4163683 4163694 ADCY9 0.011695906 1 52912109 52912134 ZCCHC11 0.011764706 11 134078847 134078858 NCAPD3 0.011764706 6 112937974 112937995 RFPL4B(dist = 265476), LOC101927686(dist = 1006742) 0.011764706 4 128814425 128814449 PLK4 0.01183432 9 34343033 34343047 NUDT2 0.01183432 14 76211938 76211949 TTLL5 0.01183432 5 150282674 150282694 ZNF300 0.011904762 16 58585178 58585191 CNOT1 0.011904762 17 1558921 1558934 PRPF8 0.011904762 19 41188890 41188901 NUMBL 0.011976048 6 17669303 17669328 NUP153 0.012048193 21 34907636 34907654 GART 0.012096774 21 42823193 42823206 MX1 0.012121212 10 93841262 93841273 CPEB3 0.012121212 10 49632498 49632510 MAPK8 0.012121212 2 167138320 167138331 SCN9A 0.012269939 22 16920145 16920157 OR11H1(dist = 470341), CCT8L2(dist = 151491) 0.012269939 7 87056260 87056297 ABCB4 0.012269939 12 111926224 111926237 ATXN2 0.012269939 8 74585483 74585494 STAU2 0.012269939 5 36123065 36123135 LMBRD2 0.012345679 6 36839451 36839462 PPIL1 0.012345679 17 40856565 40856586 EZH1 0.012345679 11 59420570 59420588 PATL1 0.012345679 12 54676165 54676176 HNRNPA1 0.012345679 5 36629801 36629815 SLC1A3 0.01242236 11 93490699 93490715 C11orf54 0.01242236 12 31289662 31289674 DDX11(dist = 31937), FAM60A(dist = 143846) 0.01242236 20 41306488 41306500 PTPRT 0.0125 1 47581121 47581151 CYP4Z1 0.0125 12 56677664 56677675 CS 0.0125 10 134628521 134628532 CFAP46 0.012578616 4 120423686 120423697 PDE5A 0.012658228 4 141481203 141481225 UCP1 0.012658228 13 25911034 25911067 NUPL1 0.012658228 11 124007701 124007714 VWA5A 0.012658228 5 134086670 134086684 CAMLG(NM_001745: c.*30_*44del0) 0.012658228 17 4712563 4712580 PLD2 0.012658228 12 122700993 122701012 DIABLO 0.012658228 4 146031236 146031253 ABCE1 0.012738854 14 39594134 39594146 GEMIN2 0.012738854 19 54264352 54264364 MIR516A2 0.012738854 12 120741303 120741326 SIRT4 0.012820513 5 14678762 14678776 OTULIN 0.012820513 1 226027067 226027104 EPHX1 0.012903226 5 153174310 153174322 GRIA1 0.012987013 9 94118279 94118310 AUH 0.012987013 17 57762402 57762414 CLTC 0.013071895 3 196532148 196532160 PAK2 0.013157895 14 53522638 53522650 DDHD1 0.013157895 12 66531936 66531947 TMBIM4 0.013333333 15 59094494 59094508 FAM63B 0.013333333 1 212217944 212217961 DTL 0.013333333 X 153714027 153714038 UBL4A 0.013333333 1 183498191 183498202 SMG7 0.013333333 4 114176848 114176860 ANK2 0.013392857 4 120192436 120192448 USP53 0.013422819 2 141272360 141272372 LRP1B 0.013422819 22 36901817 36901832 FOXRED2 0.013422819 14 60587879 60587900 PCNXL4 0.013452915 5 115167564 115167575 ATG12 0.013513514 20 60861505 60861519 OSBPL2 0.013574661 13 113818805 113818818 PROZ 0.013605442 21 47821449 47821460 PCNT 0.013605442 X 18599975 18599996 CDKL5 0.013793103 6 102130410 102130422 GRIK2 0.013888889 11 59368218 59368235 OSBP 0.013888889 16 70595514 70595525 SF3B3 0.013888889 17 61278039 61278050 TANC2 0.013888889 8 124440326 124440339 WDYHV1 0.013888889 5 137464887 137464899 NME5 0.013986014 1 236721452 236721466 HEATR1 0.013986014 16 64294574 64294585 NONE(dist = NONE), CDH11(dist = 686098) 0.014084507

TABLE 10 Microsatellite Repeat Marker Sequences for Cervical Squamous Cell Carcinoma (CESC). TABLE 10 - CESC ch start_pos end_pos CESC (hg37) (hg37) (hg37) gene p-value 12 64491002 64491019 SRGAP1 2.65648E−07 10 112360315 112360333 SMC3  1.1309E−06 7 100319680 100319696 EPO 4.50826E−06 10 18280054 18280071 SLC39A12 4.89822E−06 5 36629801 36629815 SLC1A3 8.23147E−06 15 52561891 52561907 MYO5C 9.43441E−06 22 16404838 16404857 POTEH(dist = 116901), OR11H1(dist = 43967) 9.68917E−06 11 16117684 16117698 SOX6 9.77135E−06 5 41909830 41909846 C5orf51 1.01245E−05 4 166388811 166388838 CPE 1.04949E−05 1 35885037 35885058 ZMYM4 1.08836E−05 9 97555228 97555242 C9orf3 1.36705E−05 2 87122096 87122121 ANAPC1P1 1.36705E−05 6 80910611 80910635 BCKDHB 1.42248E−05 3 160144007 160144039 SMC4 1.48093E−05 3 78695353 78695364 ROBO1 1.54264E−05 1 153617510 153617526 CHTOP 1.57816E−05 9 130243534 130243551 LRSAM1 2.40024E−05 21 34117067 34117080 PAXBP1 2.71297E−05 1 33087567 33087584 ZBTB8OS 2.79955E−05 2 230653669 230653682 TRIP12 2.79955E−05 7 128413997 128414041 OPNISW 2.79955E−05 14 76638065 76638087 GPATCH2L 3.08247E−05 10 48980563 48980577 GLUD1P7 3.08247E−05 8 22138812 22138831 PIWIL2 3.41763E−05 16 29110397 29110417 RRN3P2  3.8117E−05 X 2343183 2343213 DHRSX 4.04981E−05 12 2997058 2997074 RHNO1 4.19798E−05 7 74608740 74608754 GTF2IP1, LOC100093631 4.35346E−05 9 15472611 15472623 PSIP1 4.35346E−05 X 19024426 19024440 GPR64  5.2579E−05 17 40986454 40986487 PSME3 6.17055E−05 16 68155860 68155874 NFATC3 6.70691E−05 2 189859434 189859447 COL3A1 6.99851E−05 16 75674252 75674271 KARS 7.04722E−05 2 27463091 27463105 CAD 7.30727E−05 8 108315599 108315615 ANGPT1 7.46024E−05 6 89638988 89639004 RNGTT 8.72094E−05 3 195010023 195010035 ACAP2 8.74126E−05 10 71647196 71647209 COL13A1 9.43441E−05 17 18708830 18708843 TVP23B 0.000100728 2 66796098 66796109 MEIS1 0.000100728 2 239241445 239241460 TRAF3IP1 0.000101215 11 74053485 74053497 PGM2L1 0.000105764 18 21644075 21644099 TTC39C 0.000116891 7 92855628 92855641 HEPACAM2 0.000126456 9 163927 163943 CBWD1 0.000129634 13 28133956 28133972 LNX2 0.000135019 19 34951356 34951371 UBA2 0.000135019 3 58296209 58296232 RPP14 0.000136705 13 21370398 21370412 XPO4 0.000136705 16 12145683 12145699 SNX29 0.000186706 10 8111345 8111359 GATA3 0.000190862 6 136429995 136430013 PDE7B 0.000214777 14 90735723 90735735 PSMC1 0.000218531 12 107237602 107237626 RIC8B 0.000219298 8 22175821 22175848 PIWIL2 0.000223964 12 109510086 109510099 USP30 0.000234481 4 146031236 146031253 ABCE1 0.000238892 8 134125650 134125662 TG 0.0002442 19 54264352 54264364 MIR516A2 0.0002442 17 1383742 1383781 MYO1C 0.0002442 20 35695535 35695562 RBL1 0.000255363 6 76618182 76618195 MYO6 0.000261233 10 27333121 27333134 ANKRD26 0.00026536 8 33356825 33356839 MAK16(NM_032509: c.*678_*692del0) 0.000273598 2 166758447 166758460 TTC21B 0.000273598 3 138193025 138193038 ESYT3 0.000273598 11 68338491 68338520 PPP6R3 0.000280112 1 169845236 169845247 SCYL3 0.000280112 2 54146387 54146400 PSME4 0.000286862 19 34945331 34945344 UBA2 0.000286862 1 197059221 197059244 ASPM 0.000286862 11 18231788 18231799 LOC494141 0.000286862 19 22836873 22836886 ZNF492 0.000293858 17 27816599 27816619 TAOK1 0.000293858 3 191097928 191097944 CCDC50 0.000296187 9 19299209 19299224 DENND4C 0.000301114 3 100438778 100438810 TFG 0.000301114 16 31196218 31196237 FUS 0.000301114 4 47886322 47886342 LOC101927179 0.000301114 14 39602843 39602863 GEMIN2 0.000301114 2 201778717 201778733 ORC2 0.000308642 6 18258299 18258311 DEK 0.000308642 2 55883509 55883523 PNPT1 0.000316456 3 93768420 93768439 ARL13B 0.000316456 2 61308569 61308585 KIAA1841 0.00032457 5 118500981 118501000 DMXL1 0.00032457 11 83180169 83180185 DLG2 0.00032457 2 69553369 69553389 GFPT1 0.00032457 8 117861112 117861124 RAD21 0.00032457 14 96800846 96800858 ATG2B 0.000341763 8 17504626 17504637 MTUS1 0.000350877 1 168205770 168205781 SFT2D2 0.00036036 2 215812345 215812356 LOC101928103 0.00036036 17 40850552 40850587 CNTNAP1 0.00036075 6 55739711 55739726 BMP5(NM_021073: c.-48_-63del0) 0.000370233 5 145508515 145508535 LARS 0.000370233 4 74010555 74010571 ANKRD17 0.000380518 1 115226990 115227003 AMPD1 0.000391236 6 107420417 107420451 BEND3 0.000397875 20 49354351 49354368 PARD6B 0.000402414 3 10301805 10301816 TATDN2 0.000402414 16 31202698 31202716 FUS 0.000413223 7 98639904 98639917 SMURF1 0.000414079 8 124382376 124382403 ATAD2 0.000414079 X 48053437 48053450 SSX5 0.000414079 2 141625630 141625642 LRP1B 0.000427183 X 129546260 129546274 RBMX2 0.000437685 7 7572355 7572381 COL28A1 0.000438982 20 16025192 16025206 MACROD2 0.000438982 7 20826270 20826284 SP8 0.000438982 11 49056627 49056644 TRIM49B 0.000445931 6 100901513 100901552 SIM1 0.000445931 13 76134860 76134871 UCHL3 0.000452284 4 55131001 55131019 PDGFRA 0.00045534 20 58587783 58587794 CDH26 0.0004662 2 203817257 203817270 CARF 0.0004662 16 20803249 20803265 ACSM3, ERI2 0.0004662 2 211527815 211527840 CPS1 0.000480769 17 8417006 8417020 MYH10 0.00049584 1 144918011 144918022 NBPF20, NBPF9, PDE4DIP 0.000496032 2 88875981 88875993 EIF2AK3 0.000496032 8 121502680 121502691 MTBP 0.000496032 6 26501598 26501613 BTN1A1 0.000496032 12 54920288 54920301 NCKAP1L 0.000528821 13 113527868 113527879 ATP11A 0.000528821 X 106092450 106092473 TBC1D8B 0.000539084 8 54742095 54742107 ATP6V1H 0.000546448 1 64022708 64022725 EFCAB7 0.000549451 7 36465606 36465622 ANLN 0.000560119 3 183857809 183857826 EIF2B5 0.000560119 3 146234962 146234973 PLSCR1 0.000564972 19 39412756 39412767 SARS2 0.000580032 X 48631645 48631660 GLOD5 0.000582411 7 92900502 92900527 CCDC132 0.000584454 1 16248728 16248740 SPEN 0.000584454 9 86395372 86395398 GKAP1 0.000594059 1 155686739 155686757 DAP3 0.000594059 1 176012466 176012478 RFWD2 0.000604961 X 24516919 24516938 PDK3 0.000604961 14 55612006 55612020 LGALS3(NM_002306: c.*17_*31del0) 0.000606061 14 19571455 19571478 POTEG 0.000611154 14 102550069 102550088 HSP90AA1 0.000618429 17 1582787 1582825 PRPF8 0.000618429 18 649879 649895 TYMSOS(NM_001012716: c.*120_*104del0) 0.000618429 16 70176311 70176336 PDPR 0.00063118 X 153357614 153357628 MECP2 0.00064433 17 45105631 45105644 RPRML(dist = 49017), ARL17A(dist = 3308) 0.000649351 5 108203451 108203465 FER 0.000656111 4 141448595 141448610 ELMOD2 0.000657895 5 67584512 67584525 PIK3R1(NM_181524: c.-52_-39del-) 0.000657895 2 37487341 37487353 PRKD3 0.000671892 3 58351660 58351690 PXK 0.000686342 1 220284112 220284124 RNU5F-1 0.000686342 6 116914112 116914128 RWDD1 0.000686342 20 33225781 33225808 PIGU 0.000686342 2 238277142 238277163 COL6A3 0.000698812 12 63964640 63964653 DPY19L2 0.000701262 4 113568126 113568140 LARP7 0.000716675 14 58690427 58690451 ACTR10 0.000716675 7 131113756 131113779 MKLN1 0.000732601 7 26883761 26883776 SKAP2 0.000732601 3 58792080 58792092 C3orf67 0.000732601 X 40588605 40588618 MED14 0.000749064 3 52696310 52696322 PBRM1 0.000766088 1 39802338 39802351 MACF1 0.000766088 17 66039938 66039951 KPNA2 0.000783699 10 101992923 101992938 CWF19L1(NM_018294: c.*61_*46del0) 0.000801925 14 59790749 59790763 DAAM1 0.000801925 2 219614190 219614206 TTLL4 0.000801925 3 3194099 3194118 CRBN 0.000801925 2 44445604 44445617 PPM1B 0.000816327 21 17135361 17135372 USP25 0.000816327 1 173795803 173795821 DARS2 0.000820793 6 131211616 131211641 EPB41L2 0.000820793 X 106396617 106396641 NUP62CL 0.000840336 3 44815871 44815883 KIF15 0.000840336 1 230798864 230798876 COG2 0.000840336 1 161829973 161829987 ATF6 0.00085034 10 64022582 64022593 RTKN2 0.000860585 16 21559162 21559174 SLC7A5P2(dist = 27397), LOC101927814(dist = 41845) 0.000860585 X 52640310 52640321 XAGE1E(dist = 94113), SSX8(dist = 11664) 0.000860585 18 66367726 66367742 TMX3 0.000881575 17 57937792 57937807 TUBD1 0.000881575 4 39233719 39233734 MIR1273H 0.000903342 3 178937630 178937642 PIK3CA 0.000903342 21 17236804 17236816 USP25 0.000903342 17 30293149 30293164 SUZ12 0.000925926 15 45725103 45725138 C15orf48 0.000925926 6 117243181 117243196 RFX6 0.000925926 5 147785802 147785816 FBXO38 0.000949367 1 200080464 200080490 NR5A2 0.000965251 6 36452603 36452620 KCTD20 0.00097371 2 64112697 64112719 UGP2 0.00097371 20 47734948 47734972 STAU1 0.00097371 X 83403148 83403160 RPS6KA6 0.00097371 10 15113934 15113946 OLAH 0.00097371 10 28908452 28908478 WAC 0.00097371 2 38545608 38545626 ATL2 0.00097371 5 137507104 137507121 BRD8 0.000979792 20 13090733 13090745 SPTLC3 0.000982096 3 132169705 132169718 DNAJC13 0.000999001 16 19063220 19063235 TMC7 0.000999001 3 5024415 5024435 BHLHE40 0.000999001 6 13597295 13597307 SIRT5 0.000999001 15 86768264 86768280 AGBL1 0.001010101 11 118454476 118454495 ARCN1 0.001010101 15 82517622 82517671 EFTUD1 0.00102529 18 44424651 44424667 PIAS2 0.00102529 7 106888946 106888972 COG5 0.00102529 3 130660392 130660405 ATP2C1 0.00102529 9 99408079 99408094 AAED1 0.001038422 5 74011541 74011556 HEXB 0.001052632 5 32057910 32057923 PDZD2 0.001052632 6 49459994 49460005 CENPO(NM_018132: c.*6_*17del0) 0.001052632 3 67058329 67058357 KBTBD8 0.001081081 5 81601142 81601155 ATP6AP1L(NM_001017971: c.-79_-66del-) 0.001081081 2 236877066 236877084 AGAP1 0.001098901 18 19110456 19110477 ESCO1 0.00110742 7 95775848 95775863 SLC25A13 0.0011107 X 79991590 79991604 BRWD3 0.0011107 6 111329221 111329239 RPF2 0.001113119 11 107518175 107518187 ELMOD1 0.001141553 10 95549836 95549852 LGI1 0.001142204 1 24978892 24978909 SRRM1 0.001150599 2 201534173 201534187 AOX1 0.00116144 3 132173004 132173026 DNAJC13 0.001173709 7 75513199 75513231 RHBDD2 0.001173709 2 179442292 179442314 MIR548N, TTN-AS1 0.001173709 14 53513439 53513452 DDHD1(NM_001160148: c.*47_*34del0, 0.001207243 NM_001160147: c.*47_*34del0, NM_030637: c.*47_*34del0) 2 98907089 98907103 VWA3B 0.001207243 2 170413815 170413834 FASTKD1 0.001207243 3 138248009 138248026 CEP70 0.001242236 3 186295417 186295431 DNAJB11 0.001242236 2 178364328 178364342 AGPS 0.001242236 3 10018739 10018754 EMC3 0.001262361 3 132166148 132166162 DNAJC13 0.001278772 6 131948469 131948501 MED23 0.001315789 2 158390343 158390363 ACVR1C(NM_001111032: c.*87_*67del0, 0.001315789 NM_001111031: c.*87_*67del0, NM_001111033: c.*87_*67del0, NM_145259: c.*87_*67del0) 7 23226646 23226667 NUPL2 0.001316945 4 25160732 25160748 SEPSECS 0.001316945 6 158049351 158049365 ZDHHC14 0.001316945 1 156203572 156203588 PMF1, PMF1-BGLAP 0.001343785 9 137803188 137803208 FCN1 0.001349528 6 52768392 52768408 GSTA3 0.001356852 2 234916771 234916787 TRPM8 0.001372684 8 38839302 38839316 HTRA4 0.001372684 12 50867692 50867704 LARP4 0.001398601 19 43382540 43382581 PSG1 0.001398601 7 5087800 5087822 RBAK, RBAK-RBAKDN 0.001402525 5 128990138 128990150 ADAMTS19 0.001402525 20 30818497 30818514 POFUT1 0.001402525 1 22030115 22030132 USP48 0.001433349 17 66033401 66033412 KPNA2 0.001442308 14 104145625 104145642 KLC1 0.001442308 13 41814298 41814313 MTRF1 0.001442308 3 100016726 100016752 TBC1D23 0.001442308 11 64715330 64715349 C11orf85 0.001465201 8 103287850 103287864 UBR5 0.001488095 4 57897508 57897530 IGFBP7 0.001488095 10 81667391 81667414 LOC100288974 0.001498127 15 40509618 40509629 PAK6(NM_001128629: c.-47358_-47358delins-, 0.001501502 NM_001128628: c.-47358_-47358delins-) 12 124242458 124242472 ATP6V0A2 0.001532176 2 27597190 27597204 SNX17 0.001532176 1 197898395 197898415 LHX9(NM_001014434: c.*6_*26del0, 0.001536098 NM_020204: c.*6_*26del0) 12 56744020 56744045 STAT2 0.001536098 12 95488339 95488354 FGD6 0.001547836 X 23693084 23693098 PRDX4 0.001567398 3 138400782 138400796 PIK3CB 0.001567398 11 108141955 108141971 ATM 0.001576945 11 49196555 49196567 FOLH1 0.001586462 15 48634311 48634341 DUT(NM_001025249: c.*36_*66del0, 0.001586462 NM_001025248: c.*36_*66del0, NM_001948: c.*36_*66del0) 2 109371849 109371865 RANBP2 0.001603849 7 72159820 72159832 TYW1B 0.001603849 12 21791410 21791426 LDHB 0.001639344 5 56546749 56546777 GPBPI 0.001641587 6 34735652 34735670 SNRPC 0.001669376 8 101933023 101933037 YWHAZ 0.001680672 5 70809269 70809285 BDP1 0.001680672 2 17 36477914 36477929 MRPL45 0.001680672 18 22017875 22017901 IMPACT 0.001694915 5 14287248 14287259 TRIO 0.001694915 21 34635068 34635095 IFNAR2 0.001694915 12 43964612 43964623 ADAMTS20(dist = 18888), PUS7L(dist = 157787) 0.001753361 3 185155430 185155442 MAP3K13 0.001753361 18 61064220 61064237 VPS4B 0.001753361 9 88287588 88287615 AGTPBP1 0.001806685 4 166215662 166215692 KLHL2 0.001806685 11 27414071 27414102 LGR4 0.001806685 2 152293320 152293334 RIF1 0.001806685 1 8385485 8385496 SLC45A1 0.001806685 X 48214185 48214200 SSX3 0.001851852 21 38092247 38092259 SIM2 0.001851852 X 52654536 52654550 SSX8 0.001879699 6 136710669 136710685 MAP7 0.001893939 12 104077096 104077126 STAB2 0.001898734 2 37487307 37487330 PRKD3 0.001898734 7 54819993 54820005 SEC61G(NM_014302: c.*111_*99del0, 0.001919425 NM_001012456: c.*111_*99del0) 8 39114668 39114704 ADAM32 0.00194742 4 187627659 187627676 FAT1 0.00194742 X 129483202 129483222 SLC25A14 0.00194742 11 73984657 73984669 P4HA3 0.001948052 12 108140266 108140281 LOC101929162 0.001959686 1 229662901 229662916 ABCB10 0.001998002 2 118854094 118854108 INSIG2(NM_016133: c.-39_-25del-) 0.002016129 X 3539376 3539390 PRKX 0.002020202 17 62855003 62855017 LRRC37A3 0.002050581 19 6026288 6026302 RFX2 0.002088374 3 19959707 19959719 EFHB 0.002096436 11 68318688 68318706 PPP6R3 0.002096436 12 31289662 31289674 DDX11(dist = 31937), FAM60A(dist = 143846) 0.002162162 1 173797451 173797462 DARS2 0.002177068 7 74172385 74172400 GTF2I 0.002177068 9 133498229 133498245 FUBP3 0.002181339 5 89977095 89977106 GPR98 0.002221399 X 150573322 150573335 VMA21 0.002230167 5 94903575 94903589 ARSK 0.002230167 4 39347146 39347159 MIR1273H 0.002262443 X 77393375 77393394 TAF9B 0.002262443 20 55206241 55206253 TFAP2C 0.002280652 1 186330695 186330709 MIR548F1 0.002280652 8 42829373 42829384 HOOK3 0.002283105 11 102080325 102080341 YAP1 0.002298851 20 37146131 37146146 RALGAPB 0.002332872 17 43226461 43226506 HEXIM1(NM_006460: c.-97_-52del-) 0.002347418 3 52676065 52676079 PBRM1 0.002352941 18 30275526 30275539 KLHL14 0.002352941 15 41663884 41663900 NUSAP1 0.002386905 17 39659874 39659890 KRT13 0.002414487 5 96116095 96116125 ERAP1 0.002414487 22 46679850 46679864 TTC38 0.002442838 2 91887905 91887919 LOC654342(dist = 39930), GGT8P(dist = 75449) 0.00244898 13 102235764 102235780 ITGBL1 0.00244898 21 46602483 46602497 ADARB1 0.002500759 1 113159364 113159384 ST7L 0.002557545 5 180482303 180482317 BTNL9 0.002645503 5 147793666 147793680 FBXO38 0.002645503 1 158584103 158584116 SPTA1 0.002687444 21 33068865 33068877 SCAF4 0.002687444 3 150282051 150282075 EIF2A 0.002713704 6 7595241 7595255 SNRNP48 0.002713704 15 54586266 54586278 UNC13C 0.002754337 1 212969842 212969856 TATDN3 0.002884615 X 135115669 135115681 SLC9A6 0.002895838 7 116556086 116556111 CAPZA2 0.002895838 1 99164246 99164260 SNX7 0.002898551 12 89853387 89853405 POC1B 0.002970297 22 30051705 30051722 NF2 0.002970713 5 133707247 133707259 UBE2B(NM_003337: c.-40_-28del-) 0.002970713 15 30033645 30033656 TJP1 0.003030303 12 76780051 76780066 OSBPL8 0.00304853 17 35550269 35550290 ACACA 0.00304853 2 15536509 15536532 NBAS 0.003172924 13 113818805 113818818 PROZ 0.003278689 1 237965133 237965146 RYR2 0.003301246 11 118247264 118247277 UBE4A 0.003301246 8 59518439 59518456 NSMAF 0.003381378 10 90362299 90362324 LIPJ 0.003381378 1 155330237 155330253 ASH1L 0.003392501 17 27829588 27829602 TAOK1 0.003417635 19 37721404 37721419 ZNF383 0.003484321 20 33033065 33033083 ITCH 0.003586889 6 42611936 42611951 UBR2 0.003734483 16 69965396 69965409 WWP2 0.00381172 3 146177594 146177608 PLSCR2 0.003891377 3 142241692 142241705 ATR 0.003891377 12 81239721 81239737 LIN7A 0.003891377 19 23845789 23845807 ZNF675 0.003910927 1 3549854 3549874 WRAP73 0.003910927 2 39046321 39046333 DHX57 0.003952569 17 66038979 66038999 KPNA2 0.004140787 12 8813345 8813362 MFAP5 0.004145924 10 93752074 93752105 BTAF1 0.004145924 6 133093231 133093247 SLC18B1 0.004145924 12 72067966 72067980 THAP2 0.004152098 15 50581627 50581647 GABPB1 0.004152098 4 110433282 110433303 SEC24B 0.004236343 2 136527318 136527332 UBXN4 0.004236343 13 111076981 111076999 COL4A2 0.004236343 1 28374836 28374848 EYA3 0.004236343 5 172578549 172578567 BNIP1 0.004262575 1 155679543 155679557 DAP3 0.004426285 1 94964139 94964155 ABCD3 0.004736072 2 32427092 32427104 SLC30A6 0.004761905 8 35401930 35401941 UNC5D 0.00484659 16 24185815 24185831 PRKCB 0.005079552 X 114871127 114871141 PLS3 0.005102041 19 4297855 4297872 TMIGD2 0.005202381 1 10357206 10357224 KIF1B 0.005461791 5 68564968 68564998 CDK7 0.005461791 1 245025697 245025717 HNRNPU 0.005552794 11 88068256 88068270 CTSC 0.005598832 2 70066571 70066582 GMCL1 0.005598832 16 10783088 10783102 TEKT5 0.005649718 17 28811834 28811848 GOSR1 0.005888848 1 154227292 154227307 UBAP2L 0.005888848 18 25727760 25727775 CDH2 0.006048387 19 10741681 10741697 SLC44A2 0.006056781 17 66041871 66041886 KPNA2 0.006171026 6 24412431 24412445 MRS2 0.006540787 20 47705763 47705776 CSE1L 0.006584723 4 15826415 15826426 CD38 0.006720689 6 30154350 30154364 TRIM26 0.006896552 6 10926514 10926528 SYCP2L 0.007103491 14 96770942 96770967 ATG2B 0.007217929 1 113196179 113196217 CAPZA1 0.007519945 3 172046695 172046709 FNDC3B 0.007544507 16 4873743 4873761 GLYR1 0.007611458 15 89533168 89533181 MFGE8(dist = 76505), ABHD2(dist = 98200) 0.007832463 5 413428 413452 AHRR 0.007974115 5 72795055 72795066 BTF3 0.007974115 4 55976947 55976961 KDR 0.007998358 11 116629734 116629748 BUD13 0.008097166 14 104219578 104219590 PPP1R13B 0.008196721 5 127522153 127522180 SLC12A2 0.008395953 13 58299427 58299446 PCDH17 0.008395953 6 151859146 151859161 CCDC170 0.008807588 3 73440108 73440119 PDZRN3 0.008949965 1 65138787 65138801 CACHD1 0.009250243 4 156725681 156725695 GUCY1B3 0.009250243 8 95861778 95861797 INTS8 0.009727115 8 42323207 42323223 SLC20A2 0.009803922 9 69127139 69127155 PGM5P2 0.009992739 2 203079025 203079039 SUMO1 0.010278746 17 13399486 13399503 HS3ST3A1(NM_006042: c.*28_*11del0) 0.01048218 X 44949951 44949963 KDM6A 0.010526316 20 33665775 33665786 TRPC4AP 0.010526316 18 180211 180228 USP14 0.010638298 6 97000341 97000356 UFL1 0.010695187 X 35944077 35944088 CXorf22 0.010737856 12 56380950 56380964 RAB5B 0.010752688 10 70520707 70520747 CCARI 0.010752688 20 10273694 10273715 SNAP25 0.010869565 14 31424778 31424804 STRN3 0.010869565 17 62748076 62748093 LOC146880 0.010885341 7 47979920 47979933 PKD1L1 0.010989011 17 60374173 60374189 TBC1D3P2(dist = 21157), EFCAB3(dist = 73390) 0.011004818 2 211179765 211179777 MYL1 0.011139093 12 69214081 69214094 MDM2 0.011235955 3 57850505 57850518 SLMAP 0.011235955 X 24760276 24760289 POLA1 0.011267606 X 20204548 20204563 RPS6KA3 0.011363636 2 192011485 192011497 STAT4 0.011363636 14 104465128 104465144 TDRD9 0.011363636 6 129905035 129905050 ARHGAP18 0.011363636 12 15776223 15776244 EPS8 0.011494253 13 39435552 39435564 FREM2 0.011627907 3 180679235 180679250 FXR1 0.011627907 1 28929961 28929973 TAF12(NM_001135218: c.*90_*78del0, 0.011627907 NM_005644: c.*90_*78del0) 11 47726034 47726053 AGBL2 0.011627907 15 50754453 50754465 USP8 0.011627907 19 47700438 47700453 SAE1 0.011764706 15 33218472 33218487 FMN1 0.011764706 11 57094842 57094869 SSRP1 0.011904762 2 173861105 173861120 RAPGEF4 0.011904762 7 44715476 44715493 OGDH 0.011904762 2 219341717 219341730 USP37 0.012048193 16 28842257 28842275 ATXN2L 0.012048193 11 47701629 47701642 AGBL2 0.012048193 17 10543281 10543296 MYH3 0.012096774 3 108175734 108175745 MYH15 0.012195122 1 155671899 155671929 DAP3 0.012195122 6 31765848 31765875 LSM2 0.012195122 3 37360696 37360708 GOLGA4 0.012345679 3 108081175 108081187 HHLA2 0.012345679 X 111090289 111090311 TRPC5 0.012345679 2 228356364 228356398 AGFG1 0.012406001 2 47635523 47635537 MSH2 0.0125 3 30691871 30691882 TGFBR2 0.0125 3 137907220 137907259 ARMC8(NM_213654: c.-127_-111delins-) 0.0125 3 5249962 5249976 EDEM1 0.012658228 2 120567392 120567406 PTPN4 0.012658228 17 67178764 67178794 ABCA10 0.012658228 3 51504906 51504917 VPRBP 0.012658228 20 57611828 57611841 SLMO2-ATP5E 0.012658228 6 44216544 44216556 HSP90AB1 0.012704174 7 646958 646969 LOC101926963 0.012720908 3 108224685 108224701 MYH15 0.012820513 1 185120927 185120940 TRMT1L 0.012820513 1 65129233 65129268 CACHD1 0.012820513 14 23870220 23870234 MYH6 0.012820513 1 39751172 39751188 MACF1 0.012903226 19 36145409 36145425 COX6B1 0.012987013 4 17841869 17841881 NCAPG 0.012987013 2 33500751 33500763 LTBP1 0.012987013 14 39619587 39619599 TRAPPC6B 0.012987013 20 23473522 23473535 CST8 0.013157895 7 63673449 63673467 ZNF735 0.013157895 14 39591613 39591627 GEMIN2 0.013186884 2 207027356 207027368 EEF1B2 0.013333333 5 54552380 54552391 DHX29 0.013333333 8 120800692 120800703 TAF2 0.013333333 14 53180739 53180777 PSMC6 0.013333333 3 33339136 33339148 FBXL2 0.013333333 6 71009951 71009963 COL9A1 0.013333333 5 115628120 115628134 COMMD10 0.013420066 12 22215194 22215212 CMAS 0.013513514 21 30339205 30339217 LTN1 0.013513514 4 183600752 183600764 TENM3 0.01355087

TABLE 11 Microsatellite Repeat Marker Sequences for Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (DLBC). TABLE 11 - DLBC ch start_pos end_pos DLBC (hg37) (hg37) (hg37) gene p-value 7 66463195 66463206 TYW1 0.000112931 X 22244528 22244549 PHEX 0.000326797 1 75614380 75614410 LHX8 0.000564653 9 98230924 98230947 LOC100507346 0.000877193 4 65180308 65180357 TECRL 0.000877193 1 153907278 153907322 DENND4B 0.000877193 6 51910735 51910747 PKHD1 0.000999001 4 70280786 70280798 UGT2B28(dist = 120018), UGT2B4(dist = 65085) 0.00122549 4 73933671 73933706 COX18 0.00122549 12 117768089 117768134 NOS1 0.00128999 9 15458080 15458092 SNAPC3 0.001470588 2 233271682 233271728 ALPPL2 0.001470588 3 189690816 189690828 LEPREL1 0.001470588 3 113285185 113285212 SIDT1 0.001470588 1 155631307 155631342 YY1AP1 0.001538462 12 122097043 122097074 MORN3 0.001633987 17 39021015 39021026 KRT12 0.001785714 14 92588155 92588170 CPSF2, NDUFB1 0.001785714 12 123103008 123103016 KNTC1 0.001976285 17 13399486 13399503 HS3ST3A1(NM_006042: c.*28_*11del0) 0.001998002 1 32119347 32119376 COL16A1 0.002020202 4 143326312 143326333 INPP4B 0.002020202 21 19653342 19653355 TMPRSS15 0.002050581 1 75679569 75679580 SLC44A5 0.00210084 2 192225477 192225514 MYO1B 0.002258611 1 155737425 155737454 GON4L 0.002258611 1 43664319 43664330 CFAP57 0.002597403 17 27614746 27614770 NUFIP2 0.002597403 3 148885779 148885790 HPS3 0.002747253 3 146177594 146177608 PLSCR2 0.003007519 4 66286113 66286124 EPHA5 0.003007519 15 33915964 33915975 RYR3 0.003007519 12 1042252 1042272 RAD52 0.003030303 12 85285920 85285938 SLC6A15(NM_182767: c.-21_-39del0, 0.003095975 NM_018057: c.-21_-39del0) X 52706249 52706291 SSX7(dist = 22299), SSX2B(dist = 19655) 0.003095975 12 43964612 43964623 ADAMTS20(dist = 18888), PUS7L(dist = 157787) 0.003496503 2 113310197 113310210 POLR1B 0.003496503 20 23349607 23349618 GZF1 0.003952569 2 70066571 70066582 GMCL1 0.004127967 13 39603371 39603407 PROSER1 0.004127967 4 10027509 10027520 SLC2A9 0.004127967 11 88068256 88068270 CTSC 0.004329004 1 92944314 92944351 GFI1 0.004449388 1 38483296 38483310 UTP11L 0.004761905 3 113376110 113376147 KIAA2018 0.004901961 19 52132524 52132559 SIGLEC5 0.005263158 12 66771108 66771126 GRIP1 0.005263158 16 84121078 84121113 MBTPS1 0.005847953 6 107420417 107420451 BEND3 0.005847953 17 17039561 17039595 MPRIP 0.005882353 16 70693872 70693884 IL34 0.005882353 5 83432985 83433037 EDIL3 0.005882353 5 180663941 180663952 GNB2L1(NM_006098: c.*36_*25del0) 0.005882353 17 10411322 10411354 MYHAS 0.005882353 2 112725684 112725699 MERTK 0.005882353 17 10543281 10543296 MYH3 0.006060606 19 46815969 46815994 HIF3A 0.006060606 3 10076842 10076853 FANCD2 0.006105006 16 22579717 22579776 LOC653786 0.006105951 11 26692594 26692629 SLC5A12(NM_178498: c.*55_*20del0) 0.006302521 1 198717210 198717235 PTPRC 0.006493506 16 21991811 21991822 UQCRC2 0.006493506 2 215876589 215876603 ABCA12 0.006535948 2 61187478 61187496 PUS10 0.006535948 1 68952564 68952605 DEPDC1 0.006535948 17 28811658 28811669 GOSR1 0.006993007 15 50570999 50571024 GABPB1 0.007142857 19 22836873 22836886 ZNF492 0.007352941 1 114224782 114224799 MAGI3 0.007352941 1 54692854 54692865 SSBP3 0.007352941 3 179103328 179103352 MFN1 0.007352941 12 14949720 14949731 WBP11 0.007352941 7 134925241 134925252 STRA8 0.007518797 11 114398627 114398638 NXPE1 0.007703081 1 115276971 115276990 CSDE1 0.008333333 20 47615074 47615089 ARFGEF2 0.008333333 4 88231324 88231350 HSD17B13 0.008598572 14 50605267 50605280 SOS2 0.00862069 4 119674051 119674062 SEC24D 0.00877193 14 88651822 88651847 KCNK10(NM_138317: c.*57_*32del0, 0.00877193 NM_138318: c.*57_*32del0, NM_021161: c.*57_*32del0) 10 21177138 21177164 NEBL 0.00952381 1 236703817 236703841 LGALS8 0.00952381 4 77065476 77065492 NUP54 0.00952381 7 14028245 14028266 ETV1 0.010319917 2 227967830 227967842 COL4A4 0.010989011 12 22215194 22215212 CMAS 0.010989011 5 148207659 148207671 ADRB2(NM_000024: c.*23_*35del0) 0.010989011 7 146805220 146805232 CNTNAP2 0.010989011 3 42251577 42251608 TRAK1 0.010989011 2 271998 272015 ACP1 0.011857708 16 87935958 87935971 CA5A 0.011857708 3 183493743 183493771 YEATS2 0.011904762 10 26802633 26802648 APBB1IP 0.012820513 1 202990110 202990128 TMEM183A, TMEM183B 0.012820513 5 157180930 157180952 LSM11 0.012987013 5 122359502 122359533 PPIC(NM_000943: c.*68_*37del0) 0.013931889 4 146297387 146297396 OTUD4(dist = 196555), SMAD1(dist = 105555) 0.013986014 6 51930886 51930901 PKHD1 0.014285714 3 43756577 43756612 ABHD5 0.014285714 12 3018675 3018690 TULP3 0.014705882 17 18708830 18708843 TVP23B 0.015037594 10 115904180 115904217 CCDC186 0.015151515 4 155469959 155469971 PLRG1 0.015151515 4 110606384 110606404 CCDC109B 0.015151515 12 76461257 76461268 NAP1L1 0.015151515 13 25073399 25073415 PARP4 0.015217391 3 47143087 47143124 SETD2 0.015217391 3 154010515 154010550 DHX36 0.015737874 7 149589490 149589511 ATP6V0E2(dist = 11689), ACTR3C(dist = 354790) 0.015789474 22 16404838 16404857 POTEH(dist = 116901), OR11H1(dist = 43967) 0.016205534 3 66434357 66434397 LRIG1 0.017094017 2 139308383 139308420 SPOPL 0.017266486 2 202494630 202494642 TMEM237 0.01754386 3 186295417 186295431 DNAJB11 0.01754386 11 14539315 14539332 PSMA1 0.01754386 1 111059812 111059831 KCNA10 0.01754386 11 89914885 89914911 NAALAD2 0.01754386 2 58453843 58453856 FANCL 0.017857143 3 154002357 154002370 DHX36 0.017857143 12 107080617 107080640 LOC100287944 0.018181818 1 220789355 220789373 MARK1 0.018181818 7 114303491 114303502 FOXP2 0.018181818 6 87796161 87796171 CGA 0.018181818 2 74756111 74756122 AUP1 0.018181818 1 118623681 118623714 SPAG17 0.018351214 11 60778650 60778677 CD6 0.018461538 1 245025697 245025717 HNRNPU 0.019607843 1 175087683 175087694 TNN 0.019607843 3 125651602 125651614 ALG1L 0.019607843 12 8807982 8807993 MFAP5 0.019607843 17 53124546 53124579 STXBP4 0.019607843 10 52610342 52610369 A1CF 0.019607843 14 96770942 96770967 ATG2B 0.019762846 15 78839102 78839127 PSMA4 0.02 9 85597720 85597749 RASEF 0.021978022 2 15319070 15319084 NBAS 0.021978022 5 96342077 96342093 LNPEP 0.022058824 17 40986454 40986487 PSME3 0.022058824 1 94544805 94544830 ABCA4 0.022058824 20 52188386 52188410 ZNF217 0.022058824 X 70594925 70594942 BCYRN1 0.022222222 2 182399497 182399529 ITGA4 0.022268908 9 34017005 34017043 UBAP2 0.023715415 11 116629734 116629748 BUD13 0.023715415 17 15643372 15643392 TBC1D26 0.024242424 9 97555228 97555242 C9orf3 0.024630542 6 153292551 153292568 FBXO5 0.025 1 9770690 9770741 PIK3CD 0.025974026 4 88532182 88532215 DSPP 0.025974026 3 170857167 170857204 TNIK 0.025974026 20 29449657 29449688 NONE(dist = NONE), FRG1B(dist = 162191) 0.025974026 8 121293133 121293158 COL14A1 0.026315789 4 148457005 148457019 EDNRA 0.027568922 12 105260159 105260194 SLC41A2 0.027777778 4 46994972 46994992 GABRA4 0.028571429 2 152359276 152359297 NEB 0.028571429 10 88458996 88459025 LDB3 0.028571429 7 64004813 64004850 ZNF680 0.028571429 1 153954763 153954831 RAB13 0.028571429 10 106974123 106974140 SORCS3 0.028571429 3 47103861 47103876 SETD2 0.028571429 20 49551780 49551793 ADNP-AS1 0.028571429 1 50956053 50956192 FAF1 0.030701754 13 110859316 110859336 COL4A1 0.031578947 17 31324330 31324379 SPACA3 0.031578947 15 33256195 33256250 FMN1 0.031620553 12 9021018 9021072 A2ML1 0.031991744 11 35287000 35287014 SLC1A2 0.032967033 4 15826415 15826426 CD38 0.032967033 7 77221481 77221508 PTPN12 0.032967033 19 21558015 21558037 ZNF738 0.032967033 19 38282490 38282505 ZNF573(dist = 12260), LOC644554(dist = 25546) 0.033333333 4 110268615 110268631 COL25A1(dist = 44816), SEC24B-AS1(dist = 82488) 0.033333333 1 202107422 202107460 ARL8A 0.034443817 3 159976432 159976443 IFT80 0.035087719 21 47647618 47647632 LSS 0.035714286 3 21606027 21606040 ZNF385D-AS1 0.035714286 19 55438923 55438944 NLRP7 0.038461538 10 34985197 34985210 PARD3 0.038461538 13 31722620 31722638 HSPH1 0.039215686 21 38522344 38522368 TTC3 0.039215686 8 73983976 73984004 SBSPON 0.039215686 9 79897218 79897232 VPS13A 0.039215686 12 21639385 21639398 RECQL 0.039525692 4 96035796 96035838 BMPR1B 0.041353383 9 117803175 117803204 TNC 0.042735043 9 74349917 74349938 TMEM2 0.043290043 3 48226193 48226204 CDC25A 0.043478261 12 111701486 111701497 CUX2 0.044117647 1 24973106 24973116 SRRM1 0.044117647 3 75466006 75466019 MIR4444-1(dist = 202307), FAM86DP(dist = 4684) 0.044117647 15 31220709 31220744 FAN1 0.045454545 5 70805272 70805288 BDP1 0.045454545 14 81574687 81574712 TSHR 0.045454545 19 41798468 41798491 HNRNPUL1 0.045454545 2 128608271 128608284 POLR2D 0.045796309 7 135375909 135375932 SLC13A4 0.046153846 4 84519775 84519790 AGPAT9 0.047385621 9 32986030 32986069 APTX 0.047619048 5 130535204 130535217 LYRM7 0.047619048 17 80443296 80443308 NARF 0.047619048 5 162945387 162945400 MAT2B(NM_182796: c.*18_*31del0, 0.047619048 NM_013283: c.*18_*31del0) 3 5022981 5022992 BHLHE40 0.047619048 17 4906146 4906166 KIF1C 0.047619048 20 44512744 44512783 ZSWIM1(NM_080603: c.*55_*94del0) 0.047619048 7 102825987 102826001 DPY19L2P2 0.05 3 108102580 108102602 MYH15 0.05 18 29101215 29101231 DSG2 0.05 12 59307848 59307866 LRIG3 0.05 1 39900058 39900076 MACF1 0.05 1 114372332 114372354 AP4B1-AS1 0.05 7 882808 882841 SUN1 0.05

TABLE 12 Microsatellite Repeat Marker Sequences for Endometrial Carcinoma (UCEC). TABLE 12 - UCEC ch start_pos end_pos UCEC (hg37) (hg37) (hg37) gene p-value 7 100319680 100319696 EPO 5.87473E−48 8 103287850 103287864 UBR5 3.55758E−45 X 48214185 48214200 SSX3 1.25198E−42 10 74874082 74874112 NUDT13 3.88283E−42 2 99936265 99936280 TXNDC9 1.95768E−41 3 10018739 10018754 EMC3 7.08584E−40 20 37146131 37146146 RALGAPB 3.04311E−39 5 14485161 14485175 TRIO 4.20049E−38 7 102727051 102727067 ARMC10 7.75873E−38 2 201778717 201778733 ORC2 8.73497E−38 4 115586972 115586988 UGT8 9.83442E−38 18 180211 180228 USP14 3.60196E−37 6 111329221 111329239 RPF2 4.32986E−37 X 48631645 48631660 GLOD5 5.92777E−37 10 18280054 18280071 SLC39A12 6.63708E−37 X 20204548 20204563 RPS6KA3 1.25803E−36 5 36123065 36123135 LMBRD2 1.78204E−36 1 78432506 78432521 FUBP1 2.28578E−36 18 649879 649895 TYMSOS(NM_001012716: c.*120_*104del0) 2.63159E−36 9 104306988 104307005 RNF20 1.42702E−35 X 106092450 106092473 TBC1D8B 2.05775E−35 19 34951356 34951371 UBA2 2.56362E−35 3 129168854 129168881 IFT122 3.31279E−35 5 172578549 172578567 BNIP1 3.32569E−35 12 124242458 124242472 ATP6V0A2  5.614E−35 2 120714401 120714418 PTPN4 9.28995E−35 4 146031236 146031253 ABCE1 1.39297E−34 2 44445604 44445617 PPM1B 2.68401E−34 9 125655308 125655324 RC3H2 3.79755E−34 5 41909830 41909846 C5orf51 4.10845E−34 8 95186510 95186526 CDH17 4.12325E−34 14 53513439 53513452 DDHD1(NM_001160148: c.*47_*34del0, 4.19123E−34 NM_001160147: c.*47_*34del0, NM_030637: c.*47_*34del0) 1 39751172 39751188 MACF1  4.3787E−34 X 23693084 23693098 PRDX4 5.16618E−34 7 98639904 98639917 SMURF1 8.36556E−34 16 74372596 74372618 LOC283922 8.56745E−34 7 74608740 74608754 GTF2IP1, LOC100093631 1.43276E−33 1 39929162 39929178 MACF1 1.55105E−33 X 129267464 129267478 AIFM1 1.69459E−33 X 52654536 52654550 SSX8 1.87368E−33 1 41456808 41456823 CTPS1 3.92856E−33 10 95549836 95549852 LGI1 1.17421E−32 10 90362299 90362324 LIPJ 1.33214E−32 6 34735652 34735670 SNRPC 1.36955E−32 8 80831393 80831407 MRPS28 1.42129E−32 6 15651642 15651656 DTNBP1 1.64398E−32 11 49056627 49056644 TRIM49B 1.70778E−32 8 100160282 100160300 VPS13B 5.77233E−32 11 88068256 88068270 CTSC 5.88968E−32 3 5249962 5249976 EDEM1 6.36915E−32 13 79216356 79216381 RNF219 8.48926E−32 5 55034756 55034770 DDX4 8.71302E−32 2 55883509 55883523 PNPT1 9.02468E−32 4 44691795 44691810 GUF1 1.50215E−31 6 146256315 146256344 SHPRH 2.34454E−31 20 33225781 33225808 PIGU 2.75604E−31 X 79991590 79991604 BRWD3  2.8027E−31 6 89638988 89639004 RNGTT  3.1474E−31 9 19299209 19299224 DENND4C 3.83185E−31 9 114341239 114341255 PTGR1 6.34751E−31 15 101550861 101550877 LRRK1 7.08612E−31 3 52696310 52696322 PBRM1 9.24234E−31 X 129546260 129546274 RBMX2 9.63292E−31 12 104714847 104714867 TXNRD1 9.65902E−31 16 19063220 19063235 TMC7 1.37058E−30 9 102730697 102730712 STX17 1.58617E−30 7 114303617 114303633 FOXP2  1.6595E−30 17 30293149 30293164 SUZ12 2.84185E−30 3 196088809 196088826 UBXN7 4.16839E−30 1 173795803 173795821 DARS2 4.18459E−30 5 94842718 94842730 TTC37 4.70941E−30 X 110494528 110494543 CAPN6 5.20825E−30 12 48360947 48360961 TMEM106C 5.62633E−30 19 36145409 36145425 COX6B1 5.66865E−30 1 113159364 113159384 ST7L 5.71755E−30 3 20189528 20189540 KAT2B 6.34461E−30 2 48032740 48032754 MSH6 6.84671E−30 X 19606999 19607014 SH3KBP1 6.95349E−30 1 33087567 33087584 ZBTB8OS 7.24192E−30 13 73409508 73409522 PIBF1 8.89678E−30 4 76528928 76528945 CDKL2 1.12498E−29 2 64112697 64112719 UGP2 1.24428E−29 1 172577864 172577879 SUCO 1.27534E−29 2 179407763 179407779 MIR548N, TTN-AS1 1.47356E−29 2 178364328 178364342 AGPS 1.62863E−29 12 95488339 95488354 FGD6 1.71018E−29 6 152728079 152728093 SYNE1 1.73993E−29 5 52358761 52358775 ITGA2 2.19395E−29 6 152740681 152740695 SYNE1 2.68788E−29 22 29682873 29682894 EWSR1 2.84429E−29 10 74906122 74906136 ECD  2.8723E−29 5 132408905 132408918 HSPA4 3.38894E−29 7 135099044 135099059 CNOT4 4.04666E−29 20 58497481 58497497 SYCP2(NM_014258: c.-13_-29del0)  4.2019E−29 13 21370398 21370412 XPO4 4.95193E−29 16 70176311 70176336 PDPR 5.44704E−29 2 207027356 207027368 EEF1B2  5.7094E−29 1 114092111 114092124 MAGI3  6.3653E−29 1 176105710 176105723 RFWD2 8.23522E−29 6 97000341 97000356 UFL1 8.40277E−29 X 44949951 44949963 KDM6A 8.70466E−29 X 148582573 148582585 IDS 8.83709E−29 5 172421760 172421776 ATP6V0E1 9.22535E−29 2 203417391 203417403 BMPR2 9.23405E−29 14 76638065 76638087 GPATCH2L 9.31556E−29 X 19380975 19380993 MAP3K15 9.58034E−29 6 80910611 80910635 BCKDHB  1.0545E−28 6 17669262 17669277 NUP153 2.26794E−28 6 116912033 116912049 RWDD1 2.47805E−28 2 54146387 54146400 PSME4 2.54564E−28 1 150297334 150297351 PRPF3 2.77807E−28 1 32381592 32381607 PTP4A2 2.79089E−28 3 172052897 172052914 FNDC3B 2.89631E−28 4 141448595 141448610 ELMOD2 3.24235E−28 2 197654578 197654593 GTF3C3 3.28075E−28 6 70040500 70040513 BAI3  3.4673E−28 14 91372685 91372700 RPS6KA5 4.00986E−28 22 46679850 46679864 TTC38 4.18236E−28 7 138434066 138434081 ATP6V0A4 4.89056E−28 19 6908675 6908689 EMR1 5.27457E−28 12 96704958 96704972 CDK17 5.76102E−28 15 64496611 64496630 CSNK1G1 5.81415E−28 17 27829588 27829602 TAOK1 5.93681E−28 2 179548695 179548712 TTN 6.16285E−28 11 59626477 59626491 TCN1 6.80027E−28 2 157370018 157370033 GPD2 6.93556E−28 19 38282490 38282505 ZNF573(dist = 12260), LOC644554(dist = 25546) 7.07268E−28 7 36465606 36465622 ANLN 7.07308E−28 22 41551231 41551249 EP300 7.39952E−28 10 112360315 112360333 SMC3 7.66214E−28 12 81239721 81239737 LIN7A 8.09633E−28 12 129360344 129360381 GLT1D1 8.64142E−28 2 15536509 15536532 NBAS 1.30742E−27 5 147785802 147785816 FBXO38  1.3383E−27 6 42611936 42611951 UBR2  1.5148E−27 11 8486375 8486389 STK33 1.55137E−27 4 146046123 146046135 ABCE1 1.62305E−27 9 34017005 34017043 UBAP2 1.76307E−27 17 54981571 54981588 TRIM25 1.76981E−27 8 54742095 54742107 ATP6V1H 1.77626E−27 14 64460536 64460551 SYNE2  1.8423E−27 15 37391752 37391765 MEIS2(NM_170677: c.-85_-98del0, 1.90794E−27 NM_170676: c.-85_-98del0, NM_170675: c.-85_-98del0, NM_170674: c.-85_-98del0, NM_001220482: c.-85_-98del0) 12 57006059 57006072 BAZ2A 2.01711E−27 2 66796098 66796109 MEIS1 2.05516E−27 1 115226990 115227003 AMPD1 2.19661E−27 1 158260878 158260892 CD1C 2.63234E−27 8 39775377 39775390 IDO1 2.71157E−27 19 34945331 34945344 UBA2 2.75847E−27 2 87122096 87122121 ANAPC1P1 3.20613E−27 3 108224685 108224701 MYH15 3.61334E−27 6 88221097 88221109 SLC35A1 3.73678E−27 4 39233719 39233734 MIR1273H 3.79264E−27 2 219341717 219341730 USP37 3.94686E−27 2 64323751 64323763 PELI1 3.95947E−27 20 34435246 34435270 PHF20 4.01226E−27 15 22848150 22848166 TUBGCP5 4.46315E−27 12 42835328 42835365 PPHLN1(NM_201439: c.*17_*54del0, 5.73096E−27 NM_201440: c.*17_*54del0, NM_001143788: c.*17_*54del0, NM_001143789: c.*17_*54del0, NM_201515: c.*17_*54del0) 4 39511530 39511543 MIR1273H 5.81468E−27 7 107336262 107336274 SLC26A4  5.8531E−27 1 222904869 222904881 BROX 6.00763E−27 5 14678762 14678776 OTULIN 6.00959E−27 8 30933816 30933829 WRN 6.78308E−27 19 21350520 21350533 ZNF431  7.6725E−27 1 112305406 112305423 DDX20 7.75246E−27 8 23712066 23712089 STC1(NM_003155: c.-30_-53del0) 7.89933E−27 X 135115669 135115681 SLC9A6 9.02664E−27 7 138453892 138453909 ATP6V0A4 9.30126E−27 6 108076870 108076886 SCML4 1.00496E−26 11 125763610 125763624 PUS3(NM_001271985: c.*70_*56del0, 1.01141E−26 NM_031307: c.*70_*56del0) 12 64491002 64491019 SRGAP1 1.11012E−26 3 16636093 16636108 DAZL 1.13442E−26 6 71571688 71571707 SMAP1(NM_001281439: c.*1751_*1770del0, 1.45305E−26 NM_021940: c.*1651_*1670del0, NM_001044305: c.*1651_*1670del0, NM_001281440: c.*1651_*1670del0) 1 165712555 165712571 TMCO1 1.70207E−26 22 30051705 30051722 NF2 1.71632E−26 16 67384060 67384075 LRRC36  1.7743E−26 13 115011550 115011564 CDC16 1.78567E−26 2 236817336 236817351 AGAP1 1.83794E−26 14 75199555 75199568 FCF1 1.88459E−26 2 64331815 64331833 PELI1 2.07837E−26 1 117605130 117605145 TTF2 2.08662E−26 12 72067966 72067980 THAP2 2.30261E−26 9 133498229 133498245 FUBP3 2.56464E−26 2 228680153 228680168 CCL20 2.64191E−26 9 131456159 131456172 SET 2.85063E−26 7 64275470 64275486 ZNF138  2.8571E−26 20 35695535 35695562 RBL1  3.4436E−26 14 104465128 104465144 TDRD9 4.04883E−26 9 15472611 15472623 PSIP1 4.17961E−26 16 19619602 19619617 C16orf62 4.57527E−26 3 71008341 71008362 FOXP1(NM_001244816: c.*57_*36del0, 4.64001E−26 NM_001244812: c*57_*36del0, NM_001244813: c.*57_*36del0, NM_001244808: c.*57_*36del0, NM_001244815: c.*57_*36del0, NM_001244814: c.*57_*36del0, NM_032682: c.*57_*36del0, NM_001244810: c.*57_*36del0) 2 239241445 239241460 TRAF3IP1  4.6996E−26 6 116914112 116914128 RWDD1 4.92428E−26 2 183832100 183832113 NCKAP1 5.55817E−26 1 220369745 220369758 RAB3GAP2 5.65277E−26 2 203079025 203079039 SUMO1  7.1382E−26 7 75155143 75155157 PMS2P3 7.40022E−26 12 22215194 22215212 CMAS 7.86679E−26 1 94964139 94964155 ABCD3 8.27646E−26 6 117243181 117243196 RFX6 8.37787E−26 13 77644856 77644877 MYCBP2 8.42077E−26 4 103505784 103505799 NFKB1 9.16828E−26 17 40881033 40881048 EZH1 9.23728E−26 2 61145498 61145512 REL 9.32516E−26 2 70456452 70456465 TIA1 9.68104E−26 3 180679235 180679250 FXR1  9.8396E−26 X 44386435 44386460 FUNDC1 1.03952E−25 2 141294271 141294299 LRP1B 1.04396E−25 4 71888332 71888348 DCK 1.06332E−25 20 7921106 7921120 HAO1 1.08762E−25 1 86435957 86435971 COL24A1 1.10853E−25 3 10128965 10128985 FANCD2, FANCD2OS 1.10945E−25 17 57278908 57278920 PRR11 1.19296E−25 17 74736999 74737016 MFSD11 1.19457E−25 15 65273147 65273161 SPG21 1.38181E−25 16 24574691 24574710 RBBP6 1.38528E−25 6 20758808 20758822 CDKAL1 1.43421E−25 17 8417006 8417020 MYH10 1.53755E−25 3 172046695 172046709 FNDC3B 1.59251E−25 6 64289938 64289954 PTP4A1 1.69401E−25 9 86354663 86354679 GKAP1 1.96947E−25 12 107237602 107237626 RIC8B 2.04862E−25 6 129955151 129955165 ARHGAP18  2.062E−25 13 28133956 28133972 LNX2 2.12464E−25 1 179089233 179089251 ABL2 2.17746E−25 1 229662901 229662916 ABCB10 2.20616E−25 2 61308569 61308585 KIAA1841 2.36012E−25 12 8813345 8813362 MFAP5 2.41616E−25 12 31435608 31435620 FAM60A(NM_001135811: c.*38_*26del0, 2.57286E−25 NM_001135812: c.*38_*26del0, NM_021238: c.*38_*26del0) 3 176751870 176751887 TBL1XR1 2.59409E−25 5 96342077 96342093 LNPEP 2.61713E−25 3 160955882 160955898 NMD3 2.62196E−25 3 71739332 71739345 EIF4E3 2.79307E−25 X 117530912 117530925 WDR44 2.83955E−25 22 30772228 30772244 KIAA1656 3.03216E−25 1 99164246 99164260 SNX7 3.22713E−25 10 27333121 27333134 ANKRD26 3.24697E−25 15 40005793 40005806 FSIP1 3.24723E−25 1 46739974 46739989 RAD54L 3.55395E−25 7 7572355 7572381 COL28A1 3.75805E−25 18 43445730 43445748 EPG5 3.78319E−25 3 113222099 113222114 SPICE1 3.88128E−25 13 98634737 98634749 IPO5 3.93558E−25 1 155701055 155701071 DAP3 4.07066E−25 18 33058318 33058335 INO80C 4.12759E−25 6 64419024 64419039 PHF3  4.2205E−25 4 164440461 164440474 TMA16 4.71879E−25 10 32327037 32327053 KIF5B 4.73759E−25 6 100403812 100403827 MCHR2 4.84698E−25 10 70056619 70056632 PBLD 5.23991E−25 11 108141955 108141971 ATM 5.49788E−25 2 135887514 135887528 RAB3GAP1 5.65482E−25 X 24760276 24760289 POLA1 6.02405E−25 5 6623405 6623418 NSUN2 6.04656E−25 18 43487885 43487905 EPG5 6.28651E−25 5 180481216 180481233 BTNL9 6.99221E−25 18 6873646 6873663 ARHGAP28 7.55919E−25 4 39501722 39501754 MIR1273H 7.62153E−25 4 25315637 25315653 ZCCHC4 7.88524E−25 2 160092703 160092716 WDSUB1 7.88627E−25 8 96069973 96069988 NDUFAF6 7.94326E−25 2 74089266 74089281 STAMBP 8.17545E−25 15 42503953 42503965 TMEM87A 8.18018E−25 7 152144203 152144216 FABP5P3(dist = 4103), LINC01003(dist = 16993) 8.39608E−25 1 225707271 225707295 ENAH 8.51443E−25 18 25727760 25727775 CDH2 9.77418E−25 11 47701629 47701642 AGBL2 1.05709E−24 14 35497274 35497286 SRP54 1.12815E−24 X 138864932 138864946 ATP11C 1.19716E−24 6 53138203 53138233 ELOVL5 1.24256E−24 7 40234742 40234756 SUGCT 1.27685E−24 1 47123898 47123914 ATPAF1 1.29229E−24 6 13316780 13316795 TBC1D7 1.33818E−24 4 83376098 83376111 ENOPH1 1.37417E−24 8 67969596 67969610 COPS5 1.38893E−24 7 6064470 6064488 EIF2AK1 1.43907E−24 2 209195472 209195485 PIKFYVE  1.5602E−24 1 167871297 167871312 ADCY10 1.56745E−24 6 149846372 149846387 PPIL4  1.5972E−24 3 33626219 33626236 CLASP2 1.59992E−24 20 47649496 47649525 ARFGEF2 1.70335E−24 2 47635523 47635537 MSH2 1.70781E−24 15 52561891 52561907 MYO5C 1.78761E−24 1 247729206 247729223 GCSAML 1.79977E−24 5 78416973 78416990 BHMT 2.03856E−24 10 24784014 24784030 KIAA1217 2.15454E−24 2 120567392 120567406 PTPN4 2.26889E−24 7 63454255 63454269 MIR4283-2(dist = 372708), LINC01005(dist = 30527) 2.27302E−24 10 16824085 16824108 RSU1 2.28695E−24 1 9633387 9633400 SLC25A33 2.38094E−24 1 100542702 100542718 HIAT1 2.38209E−24 7 75185990 75186002 HIP1 2.48176E−24 8 33356825 33356839 MAK16(NM_032509: c.*678_*692del0) 2.51773E−24 12 132539500 132539513 EP400 2.52104E−24 2 192011485 192011497 STAT4 2.85475E−24 20 33033065 33033083 ITCH 2.89318E−24 14 39591613 39591627 GEMIN2 3.01178E−24 7 97939975 97939988 BAIAP2L1 3.03704E−24 1 212241691 212241730 DTL 3.12062E−24 10 21461410 21461435 NEBL 3.21502E−24 9 19334957 19334970 DENND4C 3.35705E−24 15 30010328 30010349 TJP1 3.41309E−24 X 19037666 19037686 GPR64 3.55721E−24 6 126249747 126249771 NCOA7 3.56802E−24 3 37550027 37550040 ITGA9 3.67318E−24 20 31954819 31954834 CDK5RAP1 3.77175E−24 1 95615737 95615761 TMEM56, TMEM56-RWDD3 3.83925E−24 10 94266330 94266346 IDE 3.84635E−24 3 58351660 58351690 PXK 4.06465E−24 15 63571279 63571293 APH1B 4.06645E−24 11 110128925 110128941 RDX 4.37666E−24 13 50586051 50586064 DLEU2 4.50972E−24 7 92900502 92900527 CCDC132 4.54812E−24 1 153617510 153617526 CHTOP  4.7715E−24 6 70459209 70459222 LMBRD1 4.86036E−24 6 100988266 100988280 ASCC3 4.94482E−24 7 33217071 33217084 BBS9 5.49301E−24 5 36629801 36629815 SLC1A3 5.55088E−24 9 131715001 131715017 NUP188 5.93468E−24 5 122940980 122941019 CSNK1G3 6.37687E−24 15 58974349 58974361 ADAM10 6.53338E−24 7 26883761 26883776 SKAP2 6.76383E−24 17 30500816 30500828 RHOT1 7.03669E−24 2 120620092 120620108 PTPN4 7.11287E−24 22 44083327 44083345 EFCAB6 7.12959E−24 X 52674318 52674335 SSX7 7.22303E−24 2 33586464 33586479 LTBP1 7.27653E−24 X 83403148 83403160 RPS6KA6  8.4411E−24 8 130874614 130874639 FAM49B 8.44845E−24 19 47700438 47700453 SAE1 8.49465E−24 2 55559651 55559667 CCDC88A 8.63493E−24 19 10090461 10090482 COL5A3  8.7274E−24 16 3808052 3808066 CREBBP 9.42602E−24 3 121515940 121515953 IQCB1 1.08938E−23 2 32117217 32117230 MEMO1 1.10789E−23 9 73164596 73164610 TRPM3 1.11048E−23 9 97555228 97555242 C9orf3 1.12839E−23 X 151996539 151996552 CETN2 1.15342E−23 14 68582259 68582279 RAD51B 1.16257E−23 21 30356973 30356986 LTN1  1.2089E−23 21 27136460 27136473 GABPA 1.35269E−23 7 139097271 139097295 C7orf55-LUC7L2, LUC7L2 1.38188E−23 3 132166148 132166162 DNAJC13 1.39138E−23 14 60616914 60616937 DHRS7 1.43147E−23 6 128330423 128330435 PTPRK 1.50497E−23 14 103192774 103192791 RCOR1 1.53703E−23 7 95775848 95775863 SLC25A13 1.54628E−23 8 96047806 96047820 NDUFAF6 1.56854E−23 9 21861902 21861914 MTAP 1.57606E−23 22 39079920 39079936 TOMM22(NM_020243: c.*74_*90del0) 1.58221E−23 7 107875143 107875165 NRCAM  1.6402E−23 14 23870220 23870234 MYH6 1.68664E−23 2 48734331 48734349 PPP1R21 1.69891E−23 8 30569609 30569622 GSR 1.78358E−23 13 115002097 115002111 CDC16 1.81724E−23 13 102235764 102235780 ITGBL1 1.94129E−23 8 38138934 38138975 WHSC1L1 1.94582E−23 5 134015495 134015508 SEC24A 2.00715E−23 1 173490547 173490571 SLC9C2 2.07462E−23 8 110535444 110535460 PKHD1L1 2.20731E−23 4 57897508 57897530 IGFBP7 2.25137E−23 22 16404838 16404857 POTEH(dist = 116901), OR11H1(dist = 43967) 2.26113E−23 X 19024426 19024440 GPR64 2.27979E−23 X 134033226 134033239 MOSPD1 2.32895E−23 14 35899480 35899493 NFKBIA(dist = 25520), INSM2(dist = 103755) 2.41338E−23 1 22030115 22030132 USP48 2.52505E−23 2 162081128 162081140 TANK 2.59828E−23 8 38940143 38940157 ADAM9 2.84384E−23 21 33312539 33312554 HUNK 3.05261E−23 1 233295992 233296007 PCNXL2  3.2603E−23 3 178937630 178937642 PIK3CA 3.66385E−23 6 52400479 52400497 TRAM2 3.67028E−23 1 63044645 63044661 DOCK7  3.6725E−23 12 104461711 104461723 HCFC2  3.7452E−23 1 53267474 53267488 ZYG11B 3.76262E−23 12 97051927 97051940 CDK17(dist = 257561), NEDD1(dist = 249061) 3.95815E−23 8 96260054 96260070 C8orf37 4.05657E−23 4 25160732 25160748 SEPSECS 5.03112E−23 11 18379446 18379459 GTF2H1 5.13142E−23 2 9558905 9558924 ITGB1BP1 5.37084E−23 3 124397249 124397262 KALRN  5.383E−23 5 134015250 134015288 SEC24A 5.54528E−23 3 160233406 160233421 KPNA4 5.78467E−23 7 122757719 122757733 SLC13A1 5.82457E−23 15 76205523 76205536 FBXO22 6.00755E−23 X 101409243 101409271 BEX5(NM_001159560: c.-6_-34del0,  6.0101E−23 NM_001012978: c.-6_-34del0) 2 230653669 230653682 TRIP12  6.0464E−23 10 103567665 103567680 MGEA5 6.16804E−23 6 129905035 129905050 ARHGAP18  6.4384E−23 12 4645161 4645173 C12orf4 6.63486E−23 X 15332451 15332469 ASB11 6.64968E−23 19 9771286 9771300 ZNF562 6.75884E−23 10 121675238 121675251 SEC23IP 6.85653E−23 7 29771546 29771561 DPY19L2P3(dist = 43687), WIPF3(dist = 74609) 6.91336E−23 2 48033875 48033909 MSH6 7.30708E−23 14 36334905 36334921 BRMS1L 7.31319E−23 19 327260 327277 MIER2 7.59677E−23 18 21120381 21120398 NPC1 7.88708E−23 16 75674252 75674271 KARS 7.93746E−23 2 120831654 120831667 EPB41L5 8.13895E−23 7 16676082 16676097 ANKMY2 8.78762E−23 1 231094050 231094067 TTC13 9.21226E−23 18 44424651 44424667 PIAS2 1.01973E−22 2 211521213 211521243 CPS1 1.03248E−22 5 169020337 169020350 SPDL1 1.04823E−22 12 2997058 2997074 RHNO1  1.0679E−22 6 136710669 136710685 MAP7 1.12811E−22 14 58690427 58690451 ACTR10 1.16142E−22 17 34151245 34151260 TAF15 1.18761E−22 X 114871127 114871141 PLS3 1.25087E−22 5 115167564 115167575 ATG12 1.27832E−22 11 83180169 83180185 DLG2 1.28716E−22 15 82517622 82517671 EFTUD1 1.30736E−22 12 111160513 111160526 PPP1CC 1.33503E−22 3 169992958 169992994 PRKCI 1.34012E−22 3 32571823 32571841 DYNC1LI1  1.4043E−22 8 89128708 89128722 MMP16 1.46501E−22 5 41862862 41862875 OXCT1  1.6183E−22 6 36452603 36452620 KCTD20 1.65928E−22 12 130883554 130883568 RIMBP2(NM_015347: c.*126_*112del0) 1.67958E−22 7 66747794 66747810 PMS2P4 1.81482E−22 1 11134470 11134485 EXOSC10 1.99162E−22 1 113657018 113657033 LRIG2 2.00756E−22 4 40123997 40124010 N4BP2 2.01059E−22 4 88986745 88986761 PKD2 2.10571E−22 5 118576096 118576110 DMXL1 2.14366E−22 1 207753824 207753846 CR1 2.26732E−22 15 80460576 80460591 FAH 2.27205E−22 16 22271671 22271685 EEF2K 2.32896E−22 X 135095655 135095677 SLC9A6 2.50078E−22 20 30142484 30142500 HM13 2.55811E−22 9 112184972 112184987 PTPN3 2.59524E−22 20 50292756 50292777 ATP9A 2.61241E−22 2 27597190 27597204 SNX17 2.69262E−22 X 36156447 36156461 CHDC2 2.69443E−22 14 96916232 96916246 AK7 2.76663E−22 2 234916771 234916787 TRPM8 2.80786E−22 12 76780051 76780066 OSBPL8 2.87725E−22 1 200080464 200080490 NR5A2 2.90477E−22 17 73515055 73515068 TSEN54 2.96355E−22 17 40850552 40850587 CNTNAP1 3.04468E−22 12 63964640 63964653 DPY19L2 3.05617E−22 4 151835502 151835539 LRBA 3.27142E−22 13 30854363 30854376 KATNAL1 3.28141E−22 3 138248009 138248026 CEP70 3.70122E−22 5 86679495 86679514 RASA1 3.80988E−22 21 34117067 34117080 PAXBP1 4.10987E−22 20 13140617 13140637 SPTLC3 4.21262E−22 12 110006724 110006738 MMAB 4.21923E−22 2 61577667 61577680 USP34 4.39221E−22 2 101885656 101885675 CNOT11 4.55281E−22 8 30969355 30969369 WRN 4.60908E−22 5 178030941 178030955 CLK4 4.85908E−22 6 70840124 70840137 COL19A1 4.90706E−22 2 207013834 207013846 NDUFS1 5.06749E−22 21 33982072 33982086 C21orf59 5.17312E−22 15 51768755 51768768 DMXL2 5.19323E−22 X 44918221 44918236 KDM6A 5.54968E−22 14 20763824 20763838 TTC5 5.69605E−22 17 1326754 1326769 CRK(NM_005206: c.*183_*168del0, 6.30936E−22 NM_016823: c.*53_*38del0) 2 170062201 170062216 LRP2 6.43151E−22 18 59942586 59942600 KIAA1468 6.44631E−22 15 55972660 55972674 PRTG 6.47028E−22 X 153994469 153994482 DKC1  6.8533E−22 3 132169705 132169718 DNAJC13 7.40264E−22 12 45269439 45269452 NELL2(NM_001145109: c.103_98delins-) 8.60994E−22 15 64231569 64231591 DAPK2  8.9625E−22 12 107398862 107398876 CRY1 9.27778E−22 15 52185961 52185975 TMOD3 9.41472E−22 7 35189891 35189905 DPY19L2P1 9.46007E−22 5 50122645 50122660 PARP8 9.59727E−22 15 54586266 54586278 UNC13C 9.74458E−22 4 114176848 114176860 ANK2 9.80011E−22 10 115380483 115380497 NRAP 9.84952E−22 11 121367557 121367571 SORL1 9.87851E−22 X 154133316 154133329 F8  1.0125E−21 4 42592935 42592965 ATP8A1  1.0357E−21 1 54395673 54395692 HSPB11 1.16117E−21 14 31191658 31191682 SCFD1 1.16405E−21 4 178357514 178357527 AGA 1.17267E−21 19 9361740 9361752 OR7E24 1.23798E−21 18 19119813 19119828 ESCO1 1.28329E−21 9 27062802 27062816 IFT74(NM_001099223: c.*68_*82del0, 1.31233E−21 NM_001099222: c.*68_*82del0, NM_025103: c.*68_*82del0) 12 21639528 21639542 RECOL 1.32292E−21 3 113169372 113169386 SPICE1 1.34831E−21 X 118679315 118679331 CXorf56 1.37496E−21 8 74204423 74204438 RPL7 1.40497E−21 1 155679543 155679557 DAP3  1.4121E−21 8 87111362 87111382 ATP6V0D2 1.44112E−21 8 86180906 86180924 CA13 1.46089E−21 X 154578865 154578881 LOC101927830, TMLHE-AS1 1.50205E−21 9 134049353 134049366 NUP214 1.50207E−21 6 76728583 76728598 IMPG1 1.52647E−21 5 137451460 137451472 NME5  1.5494E−21 1 84956161 84956173 RPF1 1.67924E−21 X 135481956 135481970 GPR112 1.68262E−21 2 95766553 95766567 MRPS5  1.6861E−21 20 46270911 46270923 NCOA3 1.89093E−21 14 96848565 96848580 GSKIP 1.90392E−21 1 182812410 182812425 DHX9 2.02987E−21 20 35672436 35672456 RBL1  2.0729E−21

TABLE 13 Microsatellite Repeat Marker Sequences for Kidney Renal Clear Cell Carcinoma (KIRC). TABLE 13 - KIRC ch start_pos end_pos KIRC (hg37) (hg37) (hg37) gene p-value 11 28113094 28113107 KIF18A 0.000123031 4 46994972 46994992 GABRA4 0.000124984 5 50122645 50122660 PARP8 0.000126984 6 102130410 102130422 GRIK2 0.0001638 4 170989708 170989719 AADAT 0.000219298 2 234178624 234178640 ATG16L1 0.000232919 7 103206001 103206013 RELN 0.000322027 15 40005793 40005806 FSIP1 0.000341763 7 139097271 139097295 C7orf55-LUC7L2, LUC7L2 0.000363372 15 59693969 59693985 MYO1E(dist = 28898), FAM81A(dist = 36387) 0.000380952 20 25057191 25057229 VSX1 0.000391236 11 59626477 59626491 TCN1 0.000434594 17 39871551 39871566 GAST 0.000480769 1 65138787 65138801 CACHD1 0.000571102 12 970078 970128 WNK1 0.000615214 1 235826382 235826396 LYST 0.000644053 1 36888302 36888316 OSCP1 0.000653595 9 112184972 112184987 PTPN3 0.000673325 17 39723415 39723439 KRT9 0.000701262 9 133498229 133498245 FUBP3 0.000715564 11 134054705 134054746 NCAPD3 0.000715564 2 198257652 198257684 SF3B1 0.00079968 1 75172756 75172771 CRYZ 0.000826446 12 97303682 97303713 NEDD1 0.000846323 7 63454255 63454269 MIR4283-2(dist = 372708), LINC01005(dist = 30527) 0.00089955 1 211280724 211280748 KCNH1 0.000915332 1 245021291 245021305 HNRNPU 0.000931532 3 122259738 122259756 PARP9 0.000949367 6 168348504 168348521 MLLT4 0.001052632 1 236590675 236590687 EDARADD 0.001084394 4 42626659 42626674 ATP8A1 0.001139212 13 40298620 40298639 COG6 0.001174398 5 68524006 68524019 MRPS36 0.001249844 16 69492952 69492989 CYB5B 0.0013328 14 95923421 95923440 SYNE3 0.001343785 3 191097928 191097944 CCDC50 0.00135483 11 67165932 67165942 PPP1CA(NM_002708: c.*74_*64del0, 0.001413708 NM_206873: c.*74_*64del0, NM_001008709: c.*74_*64del0) 3 10018739 10018754 EMC3 0.001439101 14 55636060 55636079 DLGAP5 0.001444788 2 179616770 179616786 TTN 0.001488095 2 189859434 189859447 COL3A1 0.001596227 15 50570999 50571024 GABPB1 0.001668057 7 138453892 138453909 ATP6V0A4 0.00172117 12 16713487 16713501 LMO3 0.001780898 4 25315637 25315653 ZCCHC4 0.001832075 4 5630470 5630482 EVC2 0.001851852 21 30910210 30910231 GRIK1 0.001893939 10 18280054 18280071 SLC39A12 0.00212073 3 172634021 172634039 SPATA16 0.002172968 12 53823175 53823189 AMHR2 0.002192982 17 17697093 17697133 RAI1 0.00255102 6 17669262 17669277 NUP153 0.002709677 10 94369023 94369100 KIF11 0.00308289 17 47109368 47109378 IGF2BP1 0.003092146 17 17152363 17152377 COPS3 0.003521914 5 172421760 172421776 ATP6V0E1 0.003583373 11 700526 700541 TMEM80 0.00381971 2 227967830 227967842 COL4A4 0.004056207 7 99711461 99711472 TAF6 0.004158416 3 131186893 131186917 MRPL3 0.004197901 1 220369745 220369758 RAB3GAP2 0.004201681 11 1905146 1905158 LSP1 0.004302926 2 215890346 215890382 ABCA12 0.005438464 2 236817336 236817351 AGAP1 0.005597933 6 41876911 41876925 MED20 0.005597933 2 183066377 183066403 PDE1A 0.005681818 11 3424760 3424773 TSSC2 0.006060606 8 42761230 42761249 HOOK3 0.00617284 20 48562797 48562813 RNF114 0.00621118 6 146256315 146256344 SHPRH 0.006289308 7 72966422 72966438 BCL7B 0.006329114 15 44024081 44024112 CKMT1A(dist = 32661), CATSPER2P1(dist = 4034) 0.006493506 1 165712555 165712571 TMCO1 0.006578947 21 35094849 35094878 ITSN1 0.006578947 5 37212582 37212612 C5orf42 0.006578947 2 54146387 54146400 PSME4 0.006622517 14 93712634 93712660 BTBD7 0.006622517 11 86120270 86120294 CCDC81 0.006666667 17 12920526 12920549 ELAC2 0.006711409 17 35979746 35979761 DDX52 0.006711409 12 2997058 2997074 RHNO1 0.006756757 11 118885668 118885701 CCDC84 0.006802721 X 20204548 20204563 RPS6KA3 0.006802721 1 176105710 176105723 RFWD2 0.006849315 14 59787325 59787338 DAAM1 0.006849315 7 64275470 64275486 ZNF138 0.006849315 1 100671860 100671880 DBT 0.006849315 10 35314130 35314161 CUL2 0.006896552 3 176751870 176751887 TBL1XR1 0.006896552 4 40123997 40124010 N4BP2 0.006896552 19 37721404 37721419 ZNF383 0.006896552 1 155671942 155671962 DAP3 0.006993007 17 465993 466012 VPS53 0.006993007 6 150123316 150123329 PCMT1 0.007063882 10 32327037 32327053 KIF5B 0.007092199 5 78416973 78416990 BHMT 0.007092199 12 42835328 42835365 PPHLN1(NM_201439: c.*17_*54del0, 0.007092199 NM_201440: c.*17_*54del0, NM_001143788: c.*17_*54del0, NM_001143789: c.*17_*54del0, NM_201515: c.*17_*54del0) 10 94266330 94266346 IDE 0.007092199 3 172052897 172052914 FNDC3B 0.007142857 20 47649496 47649525 ARFGEF2 0.007142857 8 48732074 48732096 PRKDC 0.007142857 4 94693160 94693173 GRID2 0.007194245 4 38942697 38942726 FAM114A1 0.007246377 6 18148155 18148167 TPMT 0.00729927 17 17039561 17039595 MPRIP 0.007368421 1 118623681 118623714 SPAG17 0.007406576 13 50098426 50098438 PHF11 0.007407407 X 19086800 19086823 GPR64 0.007462687 10 89720622 89720649 PTEN 0.007462687 X 119676896 119676908 CUL4B 0.007462687 14 94745068 94745095 PPP4R4(NM_058237: c.*88_*115del0) 0.007462687 2 136529897 136529910 UBXN4 0.007462687 1 149900985 149901002 MTMR11(NM_001145862: c.*36_*19del0) 0.007518797 12 72067966 72067980 THAP2 0.007518797 11 117222647 117222659 CEP164 0.007518797 4 119950975 119950989 SYNPO2 0.007567568 14 75199555 75199568 FCF1 0.007575758 7 105122891 105122924 PUS7 0.007575758 4 41015553 41015566 APBB2 0.007633588 6 42611936 42611951 UBR2 0.007633588 17 16344523 16344534 LRRC75A-AS1 0.007680492 19 7995974 7996007 TIMM44 0.007692308 11 47187055 47187087 ARFGAP2 0.007692308 1 169819526 169819538 C1orf112 0.007692308 5 36123065 36123135 LMBRD2 0.007751938 8 124817605 124817620 FAM91A1 0.007751938 17 8166113 8166126 PFAS 0.0078125 1 36019913 36019925 KIAA0319L 0.0078125 5 112903585 112903598 YTHDC2 0.007874016 2 48688258 48688273 PPP1R21 0.007874016 10 74874082 74874112 NUDT13 0.007874016 2 85589223 85589237 ELMOD3 0.007874016 2 239241445 239241460 TRAF3IP1 0.007936508 14 69861462 69861490 ERH 0.007936508 12 28412398 28412416 CCDC91 0.007936508 12 62972198 62972223 MON2 0.007936508 18 18588229 18588257 ROCK1 0.007936508 1 153949135 153949147 JTB 0.008 2 109123970 109124000 GCC2 0.008 20 50713983 50714011 ZFP64 0.008 20 47648454 47648481 ARFGEF2 0.008064516 1 36479764 36479778 AGO3 0.008064516 3 180679235 180679250 FXR1 0.008130081 6 121412191 121412203 TBC1D32 0.008196721 9 33056971 33056996 SMU1 0.008196721 8 38138934 38138975 WHSC1L1 0.008264463 1 242264075 242264108 PLD5 0.008264463 17 11697015 11697027 DNAH9 0.008333333 2 9593027 9593038 CPSF3 0.008333333 6 88126360 88126373 C6orf165 0.008333333 13 50306915 50306932 KPNA3 0.008333333 1 154144673 154144694 TPM3 0.008403361 8 120856021 120856034 DSCC1 0.008403361 7 2403894 2403908 EIF3B 0.008403361 12 97306603 97306631 NEDD1 0.008474576 5 38978758 38978770 RICTOR 0.008474576 7 151046112 151046124 NUB1 0.008474576 7 26247984 26247997 CBX3 0.008547009 2 61577667 61577680 USP34 0.008547009 6 43021976 43021989 MRPL2(NM_015950: c.*36_*23del0, 0.008598078 NM_001300848: c.*202_*189del0) 5 67584512 67584525 PIK3R1(NM_181524: c.-52_-39del-) 0.00862069 4 143181722 143181748 INPP4B 0.00862069 20 42265908 42265920 IFT52 0.00862069 4 39511530 39511543 MIR1273H 0.00877193 3 146167163 146167186 PLSCR2 0.00877193 16 31284618 31284634 ITGAM 0.00877193 12 22065994 22066028 ABCC9 0.00877193 1 161201297 161201309 NR1I3 0.00877193 20 37187110 37187134 RALGAPB 0.00877193 17 66039938 66039951 KPNA2 0.008849558 4 93225752 93225765 GRID2(NM_001286838: c.-56_-43del-, 0.008849558 NM_001510: c.-56_-43del-) 12 76453670 76453694 NAP1L1 0.008849558 2 37487307 37487330 PRKD3 0.008928571 10 76349020 76349033 ADK 0.009009009 4 47746602 47746616 CORIN 0.009090909 12 57006059 57006072 BAZ2A 0.009090909 10 90034667 90034679 RNLS(NM_018363: c.*51_*39del0) 0.009090909 3 45776875 45776914 SACM1L 0.009090909 6 105405900 105405913 LIN28B 0.009174312 16 71718538 71718563 PHLPP2 0.009174312 8 101933023 101933037 YWHAZ 0.009259259 15 50920509 50920523 TRPM7 0.009259259 6 167416662 167416676 FGFR1OP 0.009259259 2 179325203 179325214 MIR548N 0.009259259 6 39580887 39580898 KIF6 0.009259259 10 134628521 134628532 CFAP46 0.009345794 19 34945331 34945344 UBA2 0.009345794 5 59901692 59901704 DEPDC1B 0.009433962 1 22030891 22030902 USP48 0.009615385 5 150282674 150282694 ZNF300 0.009615385 7 74172385 74172400 GTF2I 0.009615385 8 130874614 130874639 FAM49B 0.009708738 7 150918586 150918602 ABCF2 0.009708738 17 4646533 4646547 ZMYND15 0.009708738 X 129265852 129265866 AIFM1 0.009708738 2 158406601 158406612 ACVR1C 0.009708738 15 34654339 34654358 LPCAT4 0.009727115 2 111881263 111881275 BCL2L11 0.009803922 15 73580950 73580962 NEO1 0.009803922 1 197009613 197009644 F13B 0.01 2 200800572 200800585 TYW5 0.01 3 185641778 185641789 TRA2B 0.01 13 45556282 45556303 NUFIP1 0.01 2 120831654 120831667 EPB41L5 0.01010101 11 113688357 113688368 USP28 0.010204082 1 32692168 32692186 EIF3I 0.010309278 2 203676382 203676403 ICA1L 0.010471204 12 112308870 112308881 MAPKAPK5 0.010638298 11 128354631 128354658 ETS1 0.010638298 12 14947675 14947706 WBP11 0.010989011 19 45540541 45540557 RELB 0.010989011 2 47600881 47600892 EPCAM 0.011111111 8 103664685 103664719 KLF10 0.011173184 10 96108988 96109000 NOC3L 0.011235955 6 44081957 44081968 MRPL14 0.011363636 6 13620380 13620391 NOL7 0.011363636 3 19498221 19498253 KCNH8 0.011494253 1 197059221 197059244 ASPM 0.011494253 16 7743418 7743437 RBFOX1 0.011560694 17 29508819 29508836 NF1 0.011560694 14 39591613 39591627 GEMIN2 0.011597333 2 70456452 70456465 TIA1 0.011627907 10 122630877 122630889 MIR5694 0.011627907 14 104040415 104040450 APOPT1 0.011627907 16 67409030 67409054 LRRC36 0.011764706 10 112649255 112649287 PDCD4 0.011764706 20 480602 480627 CSNK2A1 0.01183432 7 94181585 94181596 CASD1 0.011904762 16 31202698 31202716 FUS 0.011976048 2 45806939 45806979 SRBD1 0.012048193 1 183481943 183481964 SMG7 0.012048193 13 73547700 73547726 PIBF1 0.012048193 20 48494613 48494625 SLC9A8 0.012048193 16 4700318 4700337 MGRN1 0.012195122 12 110834030 110834049 ANAPC7 0.012195122 14 56104386 56104405 KTN1 0.012195122 1 155884155 155884167 KIAA0907 0.012269939 18 19110456 19110477 ESCO1 0.012303486 17 30500816 30500828 RHOT1 0.012345679 7 100319680 100319696 EPO 0.012345679 X 135767763 135767792 ARHGEF6 0.012345679 16 28883087 28883097 SH2B1 0.012345679 15 44778956 44778975 CTDSPL2 0.01242236 2 186689258 186689269 FSIP2 0.0125 2 98866980 98866995 VWA3B 0.0125 3 10128965 10128985 FANCD2, FANCD2OS 0.012578616 14 103192774 103192791 RCOR1 0.012578616 19 1825786 1825805 REXO1 0.012658228 4 102839351 102839362 BANK1 0.012658228 2 131883287 131883301 PLEKHB2 0.012738854 13 48828102 48828118 ITM2B 0.012738854 5 95224700 95224719 ELL2 0.012738854 1 89449508 89449520 RBMXL1 0.012820513 15 45725103 45725138 C15orf48 0.012820513 13 25911034 25911067 NUPL1 0.012820513 4 88986745 88986761 PKD2 0.012820513 10 93752074 93752105 BTAF1 0.012820513 11 77672189 77672229 INTS4 0.012820513 12 122017894 122017916 KDM2B 0.012903226 18 59942586 59942600 KIAA1468 0.012987013 12 45771901 45771918 ANO6 0.012987013 22 41551231 41551249 EP300 0.012987013 1 95615737 95615761 TMEM56, TMEM56-RWDD3 0.012987013 2 214794938 214794951 SPAG16 0.012987013 2 15676456 15676468 NBAS 0.012987013 7 150269192 150269204 GIMAP4 0.013071895 15 101019693 101019705 CERS3 0.013071895 2 111406968 111406984 BUB1 0.013071895 9 20346363 20346406 MLLT3(NM_004529: c.*78_*35del0, 0.013071895 NM_001286691: c.*78_*35del0) 10 62544391 62544411 CDK1 0.013071895 18 6975847 6975857 LAMA1 0.013157895 16 72107664 72107726 HPR 0.013157895 5 161494990 161495003 GABRG2(NM_198903: c.-16_-3del-, 0.013157895 NM_198904: c.-16_-3del-, NM_000816: c.-16_-3del-) 9 114295951 114295963 ZNF483 0.013157895 19 37581821 37581861 ZNF420 0.013245033 10 69961537 69961564 MYPN 0.013245033 2 108999483 108999515 SULT1C4 0.013245033 18 21120381 21120398 NPC1 0.013333333 9 116039089 116039115 PRPF4 0.013333333 20 61299715 61299725 SLCO4A1 0.013333333 1 113159364 113159384 ST7L 0.013422819 21 40181937 40181956 ETS2 0.013422819 14 21964623 21964635 TOX4 0.013422819 18 9279678 9279703 ANKRD12 0.013513514 2 207013834 207013846 NDUFS1 0.013513514 14 68582259 68582279 RAD51B 0.013513514 14 103449863 103449880 CDC42BPB 0.013513514 1 148594259 148594272 NBPF25P 0.013513514 20 3565277 3565289 ATRN 0.013605442 5 6623405 6623418 NSUN2 0.013605442 12 129360344 129360381 GLT1D1 0.013605442 X 138864932 138864946 ATP11C 0.013605442 1 185951573 185951589 HMCN1 0.013605442 13 77750765 77750791 MYCBP2 0.013605442 2 211179765 211179777 MYL1 0.01369863 11 63149670 63149682 SLC22A9 0.01369863 14 59790749 59790763 DAAM1 0.01369863 1 47581121 47581151 CYP4Z1 0.01369863 5 150846858 150846882 SLC36A1 0.01369863 20 47734948 47734972 STAU1 0.01369863 4 178274919 178274938 NEIL3 0.01369863 11 57505520 57505534 TMX2-CTNND1 0.01369863 8 103236408 103236428 RRM2B 0.01369863 16 74372596 74372618 LOC283922 0.013793103 7 5780521 5780558 RNF216 0.013793103 21 27136460 27136473 GABPA 0.013888889 9 86354663 86354679 GKAP1 0.013888889 7 95818864 95818897 SLC25A13 0.013888889 11 102575512 102575536 MMP27 0.013888889 4 41263718 41263729 UCHL1 0.013888889 9 13193320 13193332 MPDZ 0.013888889 2 217280250 217280286 SMARCAL1 0.013888889 20 4839890 4839911 SLC23A2 0.013986014 15 78839102 78839127 PSMA4 0.013986014 18 59942746 59942760 KIAA1468 0.013986014 1 169560727 169560740 SELP 0.013986014 20 4850568 4850578 SLC23A2 0.014084507 14 96848565 96848580 GSKIP 0.014084507 6 17292448 17292460 RBM24(NM_001143942: c.*98_*110del0, 0.014084507 NM_001143941: c.*98_*110del0, NM_153020: c.*98_*110del0) 2 120712718 120712731 PTPN4 0.014084507 1 10177680 10177693 UBE4B 0.014084507 12 62785259 62785270 USP15 0.014084507 2 162877041 162877054 DPP4 0.014084507 18 12817106 12817118 PTPN2 0.014084507 15 44002670 44002699 CKMT1A(dist = 11250), 0.014084507 CATSPER2P1(dist = 25447) 18 21047278 21047290 RIOK3 0.014084507 6 49415351 49415368 MUT 0.014184397 3 160141137 160141173 SMC4 0.014184397 16 48333493 48333512 MIR548AE2 0.014184397 2 196762491 196762509 DNAH7 0.014184397 20 37191391 37191408 RALGAPB 0.014184397 6 149846372 149846387 PPIL4 0.014184397 15 50596341 50596355 GABPB1 0.014184397 18 30275526 30275539 KLHL14 0.014184397 11 65268479 65268492 MALAT1 0.014285714 1 215914883 215914896 USH2A 0.014285714 8 53543090 53543106 RB1CC1 0.014285714 2 160092703 160092716 WDSUB1 0.014285714 1 231396485 231396509 GNPAT 0.014285714 12 108140266 108140281 LOC101929162 0.014285714 7 6064470 6064488 EIF2AK1 0.014285714 1 42776699 42776711 FOXJ3 0.014285714 12 77421978 77421991 E2F7 0.014285714 16 4861103 4861130 GLYR1 0.014285714 8 80831393 80831407 MRPS28 0.014388489 5 134305852 134305866 CATSPER3 0.014388489 3 50112589 50112605 RBM6 0.014388489 1 210414859 210414894 SERTAD4 0.014388489 15 42503953 42503965 TMEM87A 0.014492754 17 30190540 30190551 UTP6 0.014492754 2 32095023 32095056 MEMO1 0.014492754 3 108102580 108102602 MYH15 0.014492754 10 70951558 70951580 SUPV3L1 0.014492754 11 43419087 43419112 TTC17 0.014492754 3 50091941 50091957 RBM6 0.014492754 3 100378512 100378523 GPR128 0.014492754 11 119144791 119144809 CBL 0.014492754 2 197762941 197762956 PGAP1 0.014492754 9 75420448 75420463 TMC1 0.01459854 4 146031236 146031253 ABCE1 0.01459854 10 118891992 118892021 VAX1 0.01459854 7 75651305 75651336 STYXL1 0.01459854 6 138192324 138192336 TNFAIP3 0.01459854 8 39114668 39114704 ADAM32 0.01459854 5 139907713 139907738 ANKHD1, ANKHD1-EIF4EBP3 0.01459854 3 108182168 108182180 MYH15 0.01459854 6 144179190 144179202 LTV1 0.014705882 20 37395979 37396016 ACTR5 0.014705882 7 75113378 75113398 POM121C 0.014705882 12 26807065 26807090 ITPR2 0.014705882 10 120867694 120867705 FAM45B 0.014705882 1 200080464 200080490 NR5A2 0.014814815 3 37176656 37176670 LRRFIP2 0.014814815 4 128812230 128812245 PLK4 0.014814815 5 74011541 74011556 HEXB 0.014814815 2 202494630 202494642 TMEM237 0.014814815 9 135526541 135526560 DDX31 0.014814815 3 127820493 127820505 RUVBL1 0.014925373 3 186522293 186522308 RFC4 0.014925373 6 20548763 20548778 CDKAL1 0.014925373 7 122757719 122757733 SLC13A1 0.014925373 2 201470233 201470249 AOX1 0.014925373 11 59368218 59368235 OSBP 0.015037594 15 52239617 52239629 LEO1 0.015037594 12 122017848 122017866 KDM2B 0.015037594 18 29101215 29101231 DSG2 0.015037594 10 17646048 17646060 PTPLA 0.015037594 11 46568608 46568621 AMBRA1 0.015037594 9 103212778 103212790 MSANTD3, MSANTD3-TMEFF1 0.015037594 6 7575506 7575518 DSP 0.015037594 2 143913281 143913292 ARHGAP15 0.015037594 3 179298584 179298597 ACTL6A 0.015151515 1 233295992 233296007 PCNXL2 0.015151515 11 68338491 68338520 PPP6R3 0.015151515 6 117859721 117859732 DCBLD1 0.015151515 16 57494395 57494422 COQ9 0.015151515 12 54646020 54646054 CBX5 0.015151515 6 163235158 163235170 PACRG 0.015267176 11 118369265 118369290 KMT2A 0.015267176 22 26769464 26769477 SEZ6L 0.015267176 12 123103115 123103129 KNTC1 0.015267176 7 92855628 92855641 HEPACAM2 0.015267176 X 106396617 106396641 NUP62CL 0.015267176 3 194159705 194159736 ATP13A3 0.015267176 15 75909933 75909947 SNUPN 0.015267176 2 95816017 95816037 ZNF514 0.015267176 4 52928352 52928371 SPATA18 0.015348501 8 62550924 62550938 ASPH 0.015384615 17 2323953 2323979 METTL16 0.015384615 6 90452808 90452835 MDN1 0.015384615 19 55044241 55044256 KIR3DX1 0.015384615 3 160138723 160138736 SMC4 0.015384615 1 28233572 28233599 RPA2 0.015384615 4 155180652 155180681 DCHS2 0.015384615 5 180482303 180482317 BTNL9 0.015503876 3 67058329 67058357 KBTBD8 0.015503876 14 67848479 67848493 EIF2S1 0.015503876 1 92108274 92108288 CDC7(dist = 116953), TGFBR3(dist = 37612) 0.015503876 2 191155233 191155245 HIBCH 0.015503876 2 152424933 152424962 NEB 0.015625 6 89638988 89639004 RNGTT 0.015625 1 16248728 16248740 SPEN 0.015625 17 66033401 66033412 KPNA2 0.015625 X 48054294 48054306 SSX5 0.015625 8 38961268 38961280 ADAM9(NM_003816: c.*49_*61del0) 0.015625 17 57128711 57128722 TRIM37 0.015625 13 21373161 21373193 XPO4 0.015625 12 105538478 105538491 KIAA1033 0.015625 15 83805209 83805222 TM6SF1 0.015748031 6 149842148 149842176 PPIL4 0.015748031 6 51930886 51930901 PKHD1 0.015748031 12 122437594 122437605 WDR66 0.015873016 11 119145463 119145476 CBL 0.015873016 6 18258299 18258311 DEK 0.015873016 20 16359356 16359369 KIF16B 0.015873016 5 54701447 54701491 SKIV2L2 0.015873016 8 96069973 96069988 NDUFAF6 0.015873016 3 17418001 17418012 TBC1D5 0.015873016 16 53721713 53721724 RPGRIP1L 0.015873016 7 105108955 105108983 PUS7 0.015873016 2 120567392 120567406 PTPN4 0.016 1 179089233 179089251 ABL2 0.016 11 86868352 86868374 TMEM135 0.016 15 54586266 54586278 UNC13C 0.016129032 X 21534510 21534521 CNKSR2 0.016129032 2 141625834 141625854 LRP1B 0.016129032 17 74729588 74729600 METTL23 0.016129032 18 12352952 12352964 AFG3L2 0.016129032 8 59337246 59337258 UBXN2B 0.016129032 10 70506892 70506914 CCAR1 0.016129032 2 233392012 233392045 CHRND 0.016129032 X 49030763 49030811 PLP2 0.016129032 15 55972660 55972674 PRTG 0.016260163 8 67759411 67759438 C8orf44-SGK3, SGK3 0.016260163 2 152359276 152359297 NEB 0.016260163 1 197150249 197150268 ZBTB41 0.016260163 13 115007533 115007545 CDC16 0.016260163 16 4790059 4790097 C16orf71 0.016260163 2 21226218 21226230 APOB 0.016393443 6 90347394 90347406 LYRM2 0.016393443 2 61622374 61622387 USP34 0.016393443 2 169994021 169994058 LRP2 0.016393443 7 98649755 98649771 SMURF1 0.016393443 2 44934524 44934535 CAMKMT 0.016393443 13 72063066 72063077 DACH1 0.016393443 12 120295568 120295581 CIT 0.016393443 10 102716310 102716330 FAM178A 0.016528926 1 160302354 160302365 COPA 0.016528926 9 79835312 79835353 VPS13A 0.016528926 1 161326722 161326735 SDHC 0.016528926 6 8417604 8417616 SLC35B3 0.016528926 7 151884279 151884292 KMT2C 0.016528926 12 30822226 30822240 IPO8 0.016528926 1 160268834 160268846 COPA 0.016528926 9 33311294 33311306 NFX1 0.016528926 2 209113048 209113059 IDH1 0.016528926 X 135095655 135095677 SLC9A6 0.016666667 11 108332126 108332138 C11orf65 0.016666667 15 82517622 82517671 EFTUD1 0.016666667 7 24329103 24329114 NPY 0.016666667 7 106888946 106888972 COG5 0.016806723 17 57278908 57278920 PRR11 0.016806723 5 141511525 141511538 NDFIP1 0.016806723 11 75316787 75316823 MAP6(NM_207577: c.*62_*26del0) 0.016806723 6 28876873 28876904 TRIM27 0.016949153 1 161829973 161829987 ATF6 0.016949153 9 88287588 88287615 AGTPBP1 0.016949153 3 4669375 4669386 ITPR1 0.016949153 13 41382557 41382568 TPTE2P5 0.016949153 11 65270090 65270116 MALAT1 0.016949153 12 8692327 8692338 CLEC4E 0.017094017 14 35497274 35497286 SRP54 0.017241379 14 74875955 74875968 SYNDIG1L 0.017241379 1 155701055 155701071 DAP3 0.017241379 8 24348425 24348437 LOC101929294, LOC101929315 0.017391304 2 183832100 183832113 NCKAP1 0.017391304 20 16025192 16025206 MACROD2 0.017391304 2 28521140 28521152 BRE 0.017391304 15 73418741 73418756 NEO1 0.01754386 12 113645152 113645163 IQCD 0.01754386 1 46650191 46650201 TSPAN1 0.01754386 17 5324558 5324611 RPAIN 0.01754386 5 151180439 151180475 G3BP1 0.01754386 10 71055448 71055460 HK1 0.01754386 4 99802300 99802325 EIF4E 0.01754386 7 137782593 137782609 AKR1D1 0.01754386 21 30400154 30400165 USP16 0.01754386 10 91483908 91483928 KIF20B 0.01754386

TABLE 14A Microsatellite Repeat Marker Sequences for Breast Invasive Carcinoma (BRCA). TABLE 14A - BRCA ch start_pos end_pos BRCA (hg37) (hg37) (hg37) gene p-value 5 141520013 141520031 NDFIP1 7.39469E−13 17 54981571 54981588 TRIM25 1.13604E−10 22 41550984 41550996 EP300 2.74259E−10 X 52654536 52654550 SSX8 1.56045E−09 22 46679850 46679864 TTC38 2.77117E−09 20 37146131 37146146 RALGAPB 4.42782E−09 5 137498739 137498760 BRD8 4.76868E−09 6 17602786 17602812 FAM8A1  5.7796E−09 11 59626477 59626491 TCN1  1.1164E−08 12 64679694 64679708 C12orf56 1.79237E−08 13 28133956 28133972 LNX2 1.82274E−08 2 109371849 109371865 RANBP2 2.62379E−08 5 137507104 137507121 BRD8 2.85486E−08 9 19299209 19299224 DENND4C 3.94966E−08 1 98325237 98325262 TM9SF3  3.9937E−08 12 107398862 107398876 CRY1 4.03538E−08 15 65874368 65874380 VWA9 4.37731E−08 16 74920075 74920089 WDR59 5.49102E−08 2 15536509 15536532 NBAS  6.0039E−08 17 74286032 74286047 ORICH2 6.11255E−08 3 108224685 108224701 MYH15 7.07079E−08 14 91365646 91365664 RPS6KA5 9.75311E−08 6 15651642 15651656 DTNBP1 1.11363E−07 2 70456452 70456465 TLA1  1.3204E−07 2 120620092 120620108 PTPN4 1.40601E−07 18 649879 649895 TYMSOS(NM_001012716: c.*120_*104del0) 1.50586E−07 4 153268227 153268252 FBXW7 1.60586E−07 12 124242458 124242472 ATP6V0A2 1.74295E−07 3 38257551 38257583 OXSR1 1.84433E−07 7 73666736 73666750 RFC2 1.89725E−07 11 700526 700541 TMEM80 2.19644E−07 6 117026217 117026229 KPNA5 2.24588E−07 11 110128925 110128941 RDX 2.59053E−07 12 95488339 95488354 FGD6 2.62525E−07 2 85589223 85589237 ELMOD3 2.65083E−07 6 102130410 102130422 GRIK2  2.8621E−07 18 70532185 70532210 NETO1 2.89676E−07 14 56116576 56116587 KTN1 3.48417E−07 1 200080464 200080490 NR5A2 3.55386E−07 12 40258687 40258699 SLC2A13 3.68811E−07 6 131999103 131999115 ENPP3 3.96019E−07 X 44386435 44386460 FUNDC1  3.9669E−07 8 89128708 89128722 MMP16 4.23715E−07 7 2406737 2406755 EIF3B 4.50223E−07 2 101627343 101627360 RPL31, TBC1D8 4.72142E−07 5 172421760 172421776 ATP6V0E1 4.81253E−07 X 117035914 117035926 KLHL13 4.88511E−07 9 133498017 133498047 FUBP3 4.92464E−07 15 72864384 72864397 ARIH1 5.00396E−07 20 34435246 34435270 PHF20 5.51837E−07 9 131743701 131743715 NUP188 5.66832E−07 2 160092703 160092716 WDSUB1 5.68459E−07 14 39602843 39602863 GEMIN2 5.68887E−07 6 64419024 64419039 PHF3 5.69496E−07 6 131997990 131998015 ENPP3 6.23312E−07 9 135523692 135523704 DDX31 7.45582E−07 20 30142484 30142500 HM13 8.56195E−07 19 51919434 51919447 LOC100129083, SIGLEC10 8.76743E−07 4 55131001 55131019 PDGFRA 8.78839E−07 X 107827760 107827773 COL4A5 8.94998E−07 7 107336262 107336274 SLC26A4 9.33065E−07 7 23226646 23226667 NUPL2 9.65402E−07 9 100700505 100700528 HEMGN(NM_197978: c.-87_-110del0) 9.71155E−07 8 42798394 42798409 HOOK3 9.85408E−07 14 21964623 21964635 TOX4  9.9999E−07 12 62261077 62261088 FAM19A2 1.03774E−06 X 52706249 52706291 SSX7(dist = 22299), SSX2B(dist = 19655) 1.04282E−06 21 37619920 37619943 DOPEY2 1.11088E−06 6 36452603 36452620 KCTD20 1.18027E−06 9 36109839 36109853 RECK 1.25128E−06 1 22848150 22848166 TUBGCP5 1.25244E−06 8 80831393 80831407 MRPS28 1.26108E−06 5 55034756 55034770 DDX4 1.28081E−06 1 231502230 231502245 EGLN1 1.28156E−06 21 30435646 30435668 CCT8 1.31987E−06 9 5811331 5811349 ERMP1 1.32712E−06 11 8494831 8494856 STK33 1.36887E−06 X 2326742 2326763 DHRSX 1.38274E−06 5 81601142 81601155 ATP6AP1L(NM_001017971: c.-79_-66del-) 1.46347E−06 8 62557195 62557207 ASPH  1.4896E−06 9 125827752 125827764 RABGAP1 1.62925E−06 X 154133316 154133329 F8 1.71999E−06 2 207013834 207013846 NDUFS1 1.94239E−06 16 74372596 74372618 LOC283922 1.95895E−06 1 179271948 179271961 SOAT1 2.00939E−06 17 57278908 57278920 PRR11 2.09166E−06 12 53470811 53470838 SPRYD3 2.13088E−06 6 52768392 52768408 GSTA3 2.14768E−06 8 74204423 74204438 RPL7 2.25564E−06 3 160233406 160233421 KPNA4 2.39065E−06 19 47700438 47700453 SAE1  2.393E−06 2 55559651 55559667 CCDC88A 2.40511E−06 15 43307839 43307852 UBR1 2.41375E−06 17 7811876 7811889 CHD3 2.44862E−06 X 48214185 48214200 SSX3 2.50868E−06 4 113506885 113506900 ZGRF1 2.72291E−06 22 16920145 16920157 OR11H1(dist = 470341), CCT8L2(dist = 151491) 2.76507E−06 19 36145409 36145425 COX6B1 2.94377E−06 3 154002357 154002370 DHX36 3.00052E−06 10 13633928 13633944 PRPF18  3.0722E−06 8 33356825 33356839 MAK16(NM_032509: c.*678_*692del0) 3.09035E−06 14 68944343 68944358 RAD51B 3.11938E−06 6 26373465 26373491 BTN3A2  3.1902E−06 7 92020452 92020465 ANKIB1 3.20526E−06 1 172577864 172577879 SUCO 3.21437E−06 2 212495336 212495354 ERBB4 3.21515E−06 10 102019924 102019955 CWF19L1 3.25878E−06 7 50444181 50444192 IKZF1  3.275E−06 14 88454869 88454880 GALC 3.71214E−06 4 128812230 128812245 PLK4 4.08579E−06 17 1584377 1584390 PRPF8 4.11035E−06 5 86679495 86679514 RASA1 4.26896E−06 3 19959707 19959719 EFHB 4.33968E−06 4 128817905 128817919 PLK4 4.56348E−06 1 99762456 99762467 LPPR4 4.59205E−06 17 16041578 16041592 NCOR1 4.82547E−06 5 77745712 77745752 SCAMP1 4.99553E−06 10 15113934 15113946 OLAH 5.10614E−06 3 52696310 52696322 PBRM1 5.20749E−06 10 75214137 75214149 PPP3CB 5.33266E−06 1 161326722 161326735 SDHC 5.40943E−06 11 117222647 117222659 CEP164 5.41437E−06 2 183960133 183960155 DUSP19 5.55667E−06 IC 16911550 16911567 CUBN 5.60648E−06 13 79216356 79216381 RNF219  5.675E−06 X 79991590 79991604 BRWD3  5.6906E−06 5 96116095 96116125 ERAP1 5.70625E−06 3 167045701 167045723 ZBBX 5.77137E−06 2 30356973 30356986 LTN1 5.92892E−06 2 99936265 99936280 TXNDC9 5.94906E−06 4 85556378 85556414 CDS1 6.08622E−06 12 4645161 4645173 C12orf4 6.10107E−06 1 28929961 28929973 TAF12(NM_001135218: c.*90_*78del0, 6.30636E−06 NM_005644: c.*90_*78del0) 15 51017381 51017393 SPPL2A 6.30656E−06 15 63571279 63571293 APH1B 6.63087E−06 17 686296 686309 RNMTL1 6.71783E−06 16 69385403 69385421 TMED6 6.83438E−06 2 183033020 183033033 PDELA 6.95836E−06 2 203079025 203079039 SUMO1 6.97934E−06 1 25679278 25679290 TMEM50A 7.18956E−06 8 42295130 42295156 SLC20A2 7.26099E−06 2 170062201 170062216 LRP2 7.41014E−06 2 47649496 47649525 ARFGEF2 7.53143E−06 19 22836873 22836886 ZNF492 7.57428E−06 15 59974525 59974539 BNIP2  7.6175E−06 18 18619416 18619428 ROCK1 7.70041E−06 15 80460576 80460591 FAH  7.738E−06 2 200800572 200800585 TYW5 8.08649E−06 15 64717845 64717857 TRIP4 8.10818E−06 11 74053485 74053497 PGM2L1 8.18019E−06 1 93159821 93159835 EVI5 8.33371E−06 15 58974349 58974361 ADAM10 8.36316E−06 17 44833088 44833123 NSF 8.44987E−06 12 6858889 6858905 MLF2 8.57753E−06 12 81239721 81239737 LIN7A 8.61207E−06 6 149842148 149842176 PPIL4 8.61927E−06 14 60616914 60616937 DHRS7 8.79386E−06 20 4839890 4839911 SLC23A2 8.92537E−06 10 11047207 11047257 CELF2 9.06402E−06 14 64632236 64632249 MIR548AZ 9.21319E−06 18 57684454 57684466 PMAIP1(dist = 112916), MC4R(dist = 354098) 9.22399E−06 7 7572355 7572381 COL28A1 9.30353E−06 12 104461711 104461723 HCFC2 9.38876E−06 14 36218039 36218056 RALGAPA1P 9.44793E−06 1 154227292 154227307 UBAP2L 1.00433E−05 15 45725103 45725138 C15orf48 1.02325E−05 8 3611416 3611429 CSMD1 1.02542E−05 20 13140617 13140637 SPTLC3 1.06428E−05 11 8486375 8486389 STK33 1.08438E−05 9 27062802 27062816 IFT74(NM_001099223: c.*68_*82del0, 1.11177E−05 NM_001099222: c.*68_*82del0, NM_025103: c.*68_*82del0) 2 64069277 64069293 UGP2(NM_006759: c.-43-27del-) 1.12033E−05 6 146256315 146256344 SHPRH 1.12897E−05 15 83808031 83808046 HDGFRP3 1.17034E−05 5 94842718 94842730 TTC37 1.18964E−05 11 47701629 47701642 AGBL2 1.21899E−05 9 134049353 134049366 NUP214 1.26095E−05 4 146046123 146046135 ABCE1 1.31256E−05 5 16474764 16474795 FAM134B(NM_001034850: c.*86_*55del0, 1.35483E−05 NM_019000: c.*86_*55del0) 22 30772228 30772244 KIAA1656 1.41669E−05 11 88068256 88068270 CTSC 1.43837E−05 10 74874082 74874112 NUDT13 1.45304E−05 11 113697927 113697939 USP28 1.46898E−05 16 5129689 5129703 ALG1 1.49148E−05 15 50596341 50596355 GABPB1 1.49173E−05 5 180482303 180482317 BTNL9  1.4988E−05 7 74119460 74119488 LOC101926943 1.51261E−05 2 37487307 37487330 PRKD3  1.5167E−05 7 5239305 5239336 WIPI2  1.5343E−05 15 55841195 55841209 PYGO1 1.54703E−05 X 106028279 106028291 RNF128 1.54895E−05 12 53861636 53861650 PCBP2 1.63997E−05 5 72168575 72168596 TNPO1 1.65647E−05 1 202990110 202990128 TMEM183A, TMEM183B  1.6701E−05 13 103257289 103257311 TPP2 1.68273E−05 12 98989187 98989199 SLC25A3 1.70421E−05 9 19334957 19334970 DENND4C 1.74754E−05 7 65426054 65426069 GUSB 1.83556E−05 2 196738263 196738274 DNAH7 1.88079E−05 4 22444251 22444267 GPR125 1.93115E−05 11 63149670 63149682 SLC22A9  1.9384E−05 2 234916771 234916787 TRPM8 1.95462E−05 11 117152291 117152314 RNF214 1.95726E−05 1 215914883 215914896 USH2A 1.96468E−05 7 40234742 40234756 SUGCT 2.02964E−05 3 130653386 130653399 ATP2C1  2.0348E−05 4 151850226 151850239 LRBA 2.05149E−05 8 67710676 67710692 C8orf44-SGK3, SGK3 2.07821E−05 1 205129466 205129482 DSTYK 2.08628E−05 13 77792099 77792113 MYCBP2 2.11048E−05 3 122081881 122081893 CCDC58 2.14008E−05 8 38940143 38940157 ADAM9 2.20437E−05 1 117633133 117633144 TTF2  2.2361E−05 4 1701673 1701686 SLBP 2.24738E−05 4 123109034 123109048 KIAA1109 2.25353E−05 X 40588605 40588618 MED14 2.28258E−05 1 63836738 63836761 ALG6 2.32945E−05 3 186302391 186302439 DNAJB11 2.32978E−05 8 30569609 30569622 GSR 2.33037E−05 8 133854714 133854728 PHF20L1 2.33072E−05 4 159590922 159590934 C4orf46 2.37701E−05 1 109350198 109350216 STXBP3 2.39252E−05 14 58825825 58825847 ARID4A 2.39775E−05 22 40696618 40696645 TNRC6B 2.39847E−05 14 59787325 59787338 DAAM1 2.43646E−05 22 46739288 46739300 TRMU 2.43653E−05 7 98649755 98649771 SMURF1 2.47958E−05 12 42835328 42835365 PPHLN1(NM_201439: c.*17_*54del0, 2.55894E−05 NM_201440: c.*17_*54del0, NM_001143788: c.*17_*54del0, NM_001143789: c.*17_*54del0, NM_201515: c.*17_*54del0) 7 140125524 140125548 RAB19 2.55904E−05 X 52674318 52674335 SSX7  2.5792E−05 15 73409213 73409225 NEO1 2.60029E−05 14 76638065 76638087 GPATCH2L 2.61507E−05 7 131130509 131130538 MKLN1 2.65076E−05 1 38301478 38301491 MTF1 2.66706E−05 14 35242702 35242726 BAZ1A 2.66842E−05 2 61145498 61145512 REL 2.68108E−05 13 100913132 100913161 PCCA 2.69009E−05 13 77818089 77818117 MYCBP2 2.72538E−05 13 114240056 114240102 TFDP1(NM_007111: c.-64_-51delins-) 2.79044E−05 20 7921106 7921120 HAO1 2.89797E−05 17 37119364 37119376 FBXO47 2.91622E−05 20 3245219 3245232 C20orf194 2.99609E−05 11 32610726 32610740 EIF3M 3.00843E−05 14 58690427 58690451 ACTR10 3.03792E−05 X 148582573 148582585 IDS 3.04166E−05 20 48467300 48467311 SLC9A8 3.08203E−05 1 41456808 41456823 CTPS1 3.11072E−05 1 36884530 36884544 OSCP1 3.15591E−05 3 185641778 185641789 TRA2B 3.20123E−05 21 40650627 40650652 BRWD1 3.29558E−05 12 123103115 123103129 KNTC1 3.32684E−05 4 186188373 186188388 SNX25 3.38557E−05 3 69112658 69112688 UBA3 3.40289E−05 22 30367073 30367092 MTMR3  3.4236E−05 2 162849944 162849956 DPP4 3.61128E−05 6 89638988 89639004 RNGTT 3.63608E−05 18 21124907 21124917 NPC1 3.72203E−05 6 100403812 100403827 MCHR2 3.73882E−05 2 27597190 27597204 SNX17  3.7498E−05 12 93195359 93195370 EEA1 3.75154E−05 X 48054294 48054306 SSX5 3.78256E−05 6 88853530 88853542 CNR1(NM_001160259: c.*45_*33del0,  3.8126E−05 NM_001160226: c*45_*33del0, NM_001160258: c.*45_*33del0, NM_033181: c.*45_*33del0, NM_016083: c.*45_*33del0) 16 21809188 21809208 RRN3P1 4.03224E−05 1 59942586 59942600 KIAA1468 4.03953E−05 19 39909218 39909231 PLEKHG2 4.04858E−05 2 211521213 211521243 CPS1 4.07345E−05 9 118164375 118164388 DEC1 4.13609E−05 15 102287989 102288000 TARSL2(dist = 23344), OR4F6(dist = 57923) 4.14236E−05 1 90229786 90229798 PEX11A 4.21992E−05 11 16339918 16339934 SOX6 4.22764E−05 2 54146387 54146400 PSME4 4.28541E−05 2 32706267 32706279 BIRC6 4.32867E−05 1 64022708 64022725 EFCAB7 4.42689E−05 17 48202125 48202172 SAMD14 4.48308E−05 11 112832276 112832287 LOC101928847 4.50464E−05 7 107875143 107875165 NRCAM 4.52821E−05 8 95186510 95186526 CDH17 4.66014E−05 5 96093391 96093408 CAST 4.69355E−05 4 74010555 74010571 ANKRD17  4.7575E−05 2 87049358 87049371 CD8B 4.76077E−05 2 55863360 55863372 PNPT1 4.79939E−05 15 41060070 41060085 DNAJC17(NM_018163: c.*68_*53del0) 4.80818E−05 19 37155495 37155509 ZNF461 4.88873E−05 7 16704933 16704945 BZW2 4.96515E−05 11 16117684 16117698 SOX6 4.96882E−05 5 60170512 60170537 ERCC8 4.97431E−05 15 60748719 60748828 ICE2 5.02163E−05 3 129168854 129168881 IFT122 5.07038E−05 5 134086670 134086684 CAMLG(NM_001745: c.*30_*44del0) 5.07339E−05 3 71008341 71008362 FOXP1(NM_001244816: c.*57_*36del0,  5.0789E−05 NM_001244812: c.*57_*36del0, NM_001244813: c.*57_*36del0, NM_001244808: c.*57_*36del0, NM_001244815: c.*57_*36del0, NM_001244814: c.*57_*36del0, NM_032682: c.*57_*36del0, NM_001244810: c.*57_*36del0) 19 21350520 21350533 ZNF431 5.09785E−05 12 108140266 108140281 LOC101929162 5.09936E−05 12 72067966 72067980 THAP2 5.21438E−05 6 34735652 34735670 SNRPC 5.24827E−05 6 52400479 52400497 TRAM2  5.3806E−05 15 59806473 59806486 FAM81A  5.5757E−05 6 116914112 116914128 RWDD1 5.59729E−05 X 20204548 20204563 RPS6KA3 5.73558E−05 1 94212930 94212942 MRE11A 5.73564E−05 1 52242432 52242447 OSBPL9 5.76012E−05 3 10018739 10018754 EMC3 5.89287E−05 10 94366347 94366370 KIF11 5.95986E−05 X 15373247 15373259 PIR-FIGF 6.00975E−05 4 147628705 147628716 TTC29 6.01661E−05 14 45587186 45587199 FKBP3  6.0548E−05 2 74754818 74754830 AUP1 6.09097E−05 12 28459652 28459664 CCDC91 6.22686E−05 4 48529683 48529699 FRYL 6.29885E−05 14 96788613 96788623 ATG2B 6.34898E−05 2 55883509 55883523 PNPT1  6.3674E−05 8 121455551 121455586 MRPL13 6.47651E−05 17 58013510 58013529 RPS6KB1 6.57242E−05 X 3539376 3539390 PRKX 6.63723E−05 8 131812577 131812590 ADCY8  6.6825E−05 X 24084241 24084254 EIF2S3  6.7347E−05 7 100843369 100843385 MOGAT3 6.78625E−05 17 19744865 19744877 ULK2 6.79165E−05 2 29004734 29004745 PPP1CB  6.8567E−05 2 11716433 11716447 GREB1 6.89306E−05 15 43990706 43990741 CKMT1A  6.8996E−05 3 180320897 180320910 TTC14 6.99007E−05 8 28989764 28989782 KIF13B 6.99888E−05 1 39751172 39751188 MACF1 7.03684E−05 15 63447932 63447960 RPS27L 7.04191E−05 18 6873646 6873663 ARHGAP28 7.08486E−05 15 36910962 36910982 C15orf41  7.1382E−05 16 19063220 19063235 TMC7 7.15085E−05 5 14485161 14485175 TRIO 7.15971E−05 8 71037103 71037115 NCOA2 7.20881E−05 20 29633958 29633977 FRG1B  7.2897E−05 8 130874614 130874639 FAM49B 7.29254E−05 22 42415224 42415240 WBP2NL 7.34744E−05 5 34945797 34945810 DNAJC21  7.3858E−05 3 112719791 112719808 GTPBP8(NM_014170: c.*25_*42del0, 7.42669E−05 NM_138485: c.*25_*42del0) 2 203417391 203417403 BMPR2 7.47128E−05 1 220284112 220284124 RNU5F-1 7.71697E−05 6 17675386 17675402 NUP153 7.78483E−05 8 23712066 23712089 STC1(NM_003155: c.-30_-53del0) 7.84037E−05 2 230653669 230653682 TRIP12 7.98255E−05 14 20822853 20822873 PARP2  7.9997E−05 3 185155430 185155442 MAP3K13 8.02043E−05 6 80910611 80910635 BCKDHB 8.08064E−05 14 104465128 104465144 TDRD9 8.13188E−05 2 33586464 33586479 LTBP1 8.13887E−05 2 64139831 64139844 VPS54 8.15116E−05 13 113527868 113527879 ATP11A 8.32646E−05 X 1464126 1464139 IL3RA 8.41898E−05 1 110551590 110551602 AHCYL1  8.5073E−05 11 108141955 108141971 ATM 8.56614E−05 1 93584864 93584885 MTF2 8.62756E−05 2 64323751 64323763 PELI1 8.75648E−05 X 3238003 3238028 MXRA5 8.99918E−05 2 24345196 24345211 FAM228B, PFN4 9.07112E−05 1 25571794 25571805 RSRP1 9.10558E−05 5 153174310 153174322 GRIA1 9.17151E−05 3 130660392 130660405 ATP2C1 9.26142E−05 19 11411997 11412010 TSPAN16 9.35861E−05 13 48664556 48664569 MED4 9.53509E−05 11 102575512 102575536 MMP27 9.58789E−05 20 47648454 47648481 ARFGEF2 9.68143E−05 8 79629738 79629753 ZC2HC1A(NM_016010: c.*10_*25del0) 9.70187E−05 19 55044241 55044256 KIR3DX1 9.72074E−05 13 33349228 33349251 PDS5B(NM_015032: c.*38_*61del0) 9.79287E−05 3 176751870 176751887 TBL1XR1 9.79673E−05 1 118369265 118369290 KMT2A 9.86801E−05 18 29238076 29238091 B4GALT6 9.98031E−05 9 20346363 20346406 MLLT3(NM_004529: c.*78_*35del0, 0.000100456 NM_001286691: c.*78_*35del0) 9 133498229 133498245 FUBP3 0.000100818 17 19749952 19749969 ULK2 0.000101112 12 97306603 97306631 NEDD1 0.000101316 1 65099701 65099716 CACHD1 0.000101484 5 122359456 122359480 PPIC(NM_000943: c.*114_*90del0) 0.00010254  15 66794298 66794311 RPL4 0.000102816 3 3216976 3216988 CRBN 0.000102985 12 100496478 100496498 UHRF1BP1L 0.00010353  10 96317838 96317849 HELLS 0.000103543 10 32575773 32575785 EPC1 0.000103972 6 116912033 116912049 RWDD1 0.000106324 7 33192288 33192300 BBS9 0.000106487 7 16705132 16705155 BZW2 0.000107395 2 201778717 201778733 ORC2 0.000108986 13 26151184 26151196 ATP8A2 0.000109325 8 131859768 131859803 ADCY8 0.000110123 10 93784489 93784504 BTAF1 0.000110624 2 206997835 206997847 NDUFS1 0.000111763 3 169992958 169992994 PRKCI 0.000112151 6 70840124 70840137 COL19A1 0.000112286 3 146167163 146167186 PLSCR2 0.00011286  1 38052867 38052907 GNL2 0.000113072 2 165365365 165365376 GRB14 0.000113965 1 53255587 53255601 ZYG11B 0.000113969 1 49196555 49196567 FOLH1 0.000114053 1 156203572 156203588 PMF1, PMF1-BGLAP 0.000115527 10 70056619 70056632 PBLD 0.000115905 X 117530912 117530925 WDR44 0.000116052 14 55629650 55629664 DLGAP5 0.000116241 X 54042926 54042942 PHF8 0.000116241 10 101992923 101992938 CWF19L1(NM_018294: c.*61_*46del0) 0.000116687 8 74495112 74495130 STAU2 0.000116687 1 115280193 115280207 CSDE1 0.000119521 2 179478746 179478757 MIR548N, TTN-AS1 0.000121052 1 23636874 23636886 HNRNPR(NM_001102397: c.*73_*61del0, 0.000121082 NM_001102398: c.*73_*61del0, NM_001102399: c.*73_*61del0, NM_001297621: c.*73_*61del0, NM_005826: c.*73_*61del0, NM_001297622: c.*73_*61del0, NM_001297620: c.*73_*61del0) 17 57937792 57937807 TUBD1 0.000121406 8 98817552 98817571 LAPTM4B 0.000122918 15 65273147 65273161 SPG21 0.000123656 12 9706558 9706571 DDX12P(dist = 105790), KLRB1(dist = 41299) 0.000124364 8 68140383 68140394 ARFGEF1 0.000124626 11 46666872 46666883 ATG13 0.000125707 7 21646233 21646254 DNAH11 0.000125754 8 134125650 134125662 TG 0.000126143 12 118463653 118463672 RFC5 0.000128595 13 25467010 25467036 CENPJ 0.000129675 7 95775848 95775863 SLC25A13 0.000129763 12 54963479 54963504 PDE1B 0.000130574 8 30933816 30933829 WRN 0.000130739 9 3937244 3937266 GLIS3 0.000131271 7 131113756 131113779 MKLN1 0.000131353 2 102959416 102959427 IL1RL1 0.000137854 2 48046012 48046035 FBXO11 0.000138729 6 44216544 44216556 HSP90AB1 0.000138791 2 61456592 61456645 USP34 0.000140362 3 52676065 52676079 PBRM1 0.000141221 11 86120270 86120294 CCDC81 0.000141469 16 69293926 69293945 SNTB2 0.000141826 5 76707435 76707447 PDE8B 0.000141841 15 101019693 101019705 CERS3 0.000142232 1 241954005 241954024 WDR64 0.000142972 4 39511530 39511543 MIR1273H 0.000143658 5 170818290 170818301 NPM1 0.000144503 10 52502803 52502820 ASAH2B 0.000144537 17 33288433 33288445 CCT6B(NM_001193530: c.-21_-33del0, 0.00014505  NM_001193529: c.-21_-33del0, NM_006584: c.-21_-33del0) 14 72941317 72941328 RGS6 0.000147191 6 17669262 17669277 NUP153 0.000147437 13 24410498 24410511 MIPEP 0.000147674 2 60988862 60988872 PAPOLG 0.000150282 1 153516162 153516173 S100A4(NM_019554: c.*73_*62del0, 0.000150567 NM_002961: c.*73_*62del0) 14 39594134 39594146 GEMIN2 0.000151984 2 158275111 158275135 CYTIP 0.000153201 7 77006696 77006740 GSAP 0.000153239 11 119145463 119145476 CBL 0.000153271 6 100006295 100006309 CCNC 0.000153773 19 42213456 42213487 CEACAM5 0.000154108 6 8417604 8417616 SLC35B3 0.00015465  5 32057910 32057923 PDZD2 0.000155854 8 103287850 103287864 UBR5 0.000156041 4 40123997 40124010 N4BP2 0.000156489 7 64004813 64004850 ZNF680 0.000158124 16 3558262 3558286 CLUAP1 0.00015942  15 50782416 50782446 USP8 0.000159535 5 145888687 145888714 TCERG1 0.000160126 X 48156078 48156097 SSX1(dist = 29199), SSX9(dist = 4888) 0.000160216 11 104869775 104869786 CASP5 0.000160312 5 41862862 41862875 OXCT1 0.000160345 17 65919172 65919190 BPTF 0.00016091  17 29192700 29192715 ATAD5 0.000161778 5 137506862 137506874 BRD8 0.000164042 1 28218773 28218784 RPA2 0.000164065 17 16137244 16137257 PIGL 0.000164626 16 31284618 31284634 ITGAM 0.000164629 2 100035414 100035425 REV1 0.000164645 6 56504477 56504489 RNU6-71P 0.000165004 7 44663890 44663910 OGDH 0.000165068 14 50050396 50050408 RPS29 0.000165132 20 43623620 43623658 STK4 0.000167071 15 65847112 65847125 PTPLAD1 0.000168471 17 2323953 2323979 METTL16 0.000169004 12 31820564 31820578 METTL20 0.000169079 17 62855003 62855017 LRRC37A3 0.000169397 11 5687320 5687338 TRIM5 0.000171126 7 54819993 54820005 SEC61G(NM_014302: c.*111_*99del0, 0.000171145 NM_001012456: c.*111_*99del0) 5 150856066 150856091 SLC36A1 0.000176203 7 135098181 135098192 CNOT4 0.000176239 5 72875091 72875102 UTP15 0.000179126 19 16591361 16591374 CALR3 0.000179261 17 10543281 10543296 MYH3 0.000180269 10 74653468 74653479 OIT3(NM_152635: c.-89_-78del-) 0.000182549 6 138192324 138192336 TNFAIP3 0.000185237 2 119748135 119748152 MARCO 0.000188321 1 207753824 207753846 CR1 0.000190019 14 92549604 92549623 ATXN3 0.000191433 3 137981439 137981456 ARMC8, NME9 0.000192654 5 112346416 112346447 DCP2 0.000192739 1 176050430 176050447 RFWD2 0.000193515 18 9954233 9954247 VAPA(NM_003574: c.*25_*39del0, 0.000193536 NM_194434: c.*25_*39del0) 5 177676986 177677011 COL23A1 0.000193663 12 46758392 46758417 SLC38A2 0.000194061 15 41364265 41364305 INO80 0.000196303 17 27816599 27816619 TAOK1 0.000196406 21 34655334 34655346 IL10RB 0.000196457 12 110006724 110006738 MMAB 0.000197329 4 8176744 8176762 ABLIM2(dist = 16185), SH3TC1(dist = 24298) 0.000198718 6 84649715 84649747 CYB5R4 0.000199255 5 180481216 180481233 BTNL9 0.000201144 3 178937630 178937642 PIK3CA 0.000201385 4 39233719 39233734 MIR1273H 0.000201789 4 76528928 76528945 CDKL2 0.000204475 20 46266543 46266558 NCOA3 0.000206036 6 138628598 138628611 KIAA1244 0.00020697  1 22030115 22030132 USP48 0.000209782 2 55874657 55874673 PNPT1 0.000210064 11 102272460 102272474 TMEM123 0.000211224

TABLE 14B Microsatellite Repeat Marker Sequences for Breast Invasive Carcinoma (BRCA), top 501-800. TABLE 14B - BRCA (top 501-800) ch start_pos end_pos BRCA (hg37) (hg37) (hg37) gene p-value 7 6064470 6064488 EIF2AK1 0.000215139 1 109525421 109525434 WDR47 0.00021611 3 191888452 191888477 FGF12 0.000216675 1 144923886 144923908 NBPF20, NBPF9, PDE4DIP 0.000217108 11 73753268 73753288 C2CD3 0.000218485 6 30573637 30573656 PPP1R10 0.000220796 21 32597972 32597988 TIAM1 0.000221172 1 197150249 197150268 ZBTB41 0.00022148 7 63454255 63454269 MIR4283-2(dist = 372708), 0.000223592 LINC01005(dist = 30527) 13 73293238 73293264 MZT1 0.00022874 13 98634737 98634749 IPO5 0.000230862 12 112308870 112308881 MAPKAPK5 0.000231363 9 98009613 98009626 FANCC 0.000231592 10 7747034 7747047 ITIH2 0.000234104 3 108081175 108081187 HHLA2 0.000234278 18 180211 180228 USP14 0.000236119 7 77221481 77221508 PTPN12 0.000236394 7 87516629 87516640 DBF4 0.000236508 10 99197102 99197124 EXOSC1 0.000238254 2 206630073 206630104 NRP2 0.000238549 7 104707158 104707171 KMT2E 0.000238915 7 89982116 89982127 GTPBP10 0.000240015 8 101725020 101725049 PABPC1 0.00024033 9 78638564 78638576 PCSK5 0.000240635 9 71538318 71538330 PIP5K1B 0.000240872 19 56329186 56329204 NLRP11 0.000241089 1 86435957 86435971 COL24A1 0.000241824 14 75497428 75497440 MLH3 0.000243816 12 19410474 19410488 PLEKHA5 0.000244258 5 36629801 36629815 SLC1A3 0.000245173 12 48360947 48360961 TMEM106C 0.000245589 2 189926219 189926240 COL5A2 0.000245777 5 65088487 65088503 NLN 0.000246233 6 121412191 121412203 TBC1D32 0.000246816 6 148761410 148761421 SASH1 0.000248157 1 245021291 245021305 HNRNPU 0.000248446 X 1467519 1467589 IL3RA 0.000249364 5 118451836 118451847 DMXL1 0.000253336 19 34951356 34951371 UBA2 0.000255632 14 45716018 45716030 MIS18BP1 0.000255938 7 74608740 74608754 GTF2IP1, LOC100093631 0.000256607 11 73429947 73429972 RAB6A 0.000259703 16 31435918 31435935 ITGAD 0.00026029 5 134305852 134305866 CATSPER3 0.000261255 4 146031236 146031253 ABCE1 0.000263404 6 7410735 7410747 RIOK1 0.000266156 4 44691795 44691810 GUF1 0.000266198 11 107518175 107518187 ELMOD1 0.000266907 2 114691775 114691788 ACTR3 0.000267567 1 100624000 100624012 LRRC39 0.000268684 12 77421978 77421991 E2F7 0.000270478 12 31289662 31289674 DDX11(dist = 31937), 0.00027167 FAM60A(dist = 143846) 2 112625555 112625566 ANAPC1 0.000273396 19 10288056 10288083 DNMT1 0.0002743 3 33725814 33725828 CLASP2 0.000277579 1 70904523 70904552 CTH 0.000278482 7 23239063 23239074 NUPL2 0.000285563 3 179481971 179482004 USP13 0.000285752 19 12543765 12543777 ZNF443 0.00028884 5 33561022 33561043 ADAMTS12 0.000290387 19 33406199 33406229 CEP89 0.000293182 3 180679235 180679250 FXR1 0.000294248 7 95864044 95864057 SLC25A13 0.000295824 19 18453807 18453828 PGPEP1 0.000296643 6 37328387 37328414 RNF8 0.000300188 3 138248009 138248026 CEP70 0.000300509 19 21116763 21116804 ZNF85 0.000301771 5 98224945 98224957 CHD1 0.000304934 9 73479430 73479465 TRPM3 0.000305947 12 89995053 89995065 ATP2B1 0.000306087 2 238005446 238005457 COPS8 0.000307607 4 107037269 107037282 TBCK 0.000308459 1 117605130 117605145 TTF2 0.000310064 10 26825151 26825168 APBB1IP 0.000310141 8 63948170 63948202 GGH 0.000310478 14 71517327 71517341 PCNX 0.000310486 3 121515940 121515953 IQCB1 0.00031238 X 67741418 67741434 YIPF6 0.000321373 2 186689258 186689269 FSIP2 0.000322176 3 93768420 93768439 ARL13B 0.000323021 6 90503754 90503779 MDN1 0.000324941 15 76205523 76205536 FBXO22 0.000325112 2 118860645 118860670 INSIG2 0.000325658 6 135286438 135286451 HBS1L 0.000326898 19 7119636 7119690 INSR 0.000331431 2 111721142 111721186 ACOXL 0.000332494 12 105540322 105540335 KIAA1033 0.000333725 6 139598061 139598085 TXLNB 0.000334997 14 20857306 20857321 TEP1 0.000335308 2 228159652 228159677 LOC654841 0.000337791 3 100992404 100992415 IMPG2 0.00033855 21 33979904 33979922 C21orf59 0.000339462 14 35899480 35899493 NFKBIA(dist = 25520), 0.000340538 INSM2(dist = 103755) 5 139907750 139907762 ANKHD1, ANKHD1-EIF4EBP3 0.000340919 19 22585521 22585535 ZNF98 0.000341515 14 81574687 81574712 TSHR 0.000341771 X 110494528 110494543 CAPN6 0.000343324 13 49684436 49684450 FNDC3A 0.000343963 4 123374811 123374832 IL2 0.000345147 1 154178185 154178198 C1orf189 0.000345147 9 77457028 77457044 TRPM6 0.000347826 20 48562797 48562813 RNF114 0.000349748 2 62063093 62063111 FAM161A 0.000350662 2 66796098 66796109 MEIS1 0.000353069 2 28464369 28464382 BRE 0.00035345 19 10270725 10270758 DNMT1 0.000353765 9 86354663 86354679 GKAP1 0.00035517 6 11192516 11192554 NEDD9 0.000355793 12 21639528 21639542 RECQL 0.000357453 5 137451460 137451472 NME5 0.000358028 21 33068865 33068877 SCAF4 0.000360163 20 47770443 47770478 STAU1 0.000360337 20 37126168 37126180 RALGAPB 0.000361914 1 181714466 181714481 CACNA1E 0.000363372 3 111873902 111873917 SLC9C1 0.000368608 7 87056260 87056297 ABCB4 0.000369293 15 73567127 73567163 NEO1 0.000369773 1 14057425 14057439 PRDM2 0.000370053 6 10989873 10989887 ELOVL2 0.00037325 15 49064607 49064620 CEP152 0.000373471 8 22138812 22138831 PIWIL2 0.000374497 14 75476004 75476015 EIF2B2 0.00037452 8 67759411 67759438 C8orf44-SGK3, SGK3 0.000375342 12 101598350 101598362 SLC5A8 0.000378825 3 132166148 132166162 DNAJC13 0.000382559 12 132539500 132539513 EP400 0.000383983 1 94230106 94230131 ANKRD49 0.000385032 15 70963344 70963368 UACA 0.000385269 3 171455451 171455462 PLD1 0.000385719 19 36572251 36572263 WDR62 0.000386586 2 192011485 192011497 STAT4 0.00038737 3 119348345 119348362 PLA1A 0.000387842 X 153357614 153357628 MECP2 0.000393618 16 19619602 19619617 C16orf62 0.00039685 22 29682873 29682894 EWSR1 0.000397816 3 65361369 65361402 MAGI1 0.000399074 6 32123361 32123410 PPT2-EGFL8 0.000402145 3 124998098 124998118 ZNF148 0.000403189 1 109856836 109856854 SORT1 0.000407145 15 51768755 51768768 DMXL2 0.000407952 2 190321967 190321989 WDR75 0.000412862 1 225607366 225607387 LBR 0.000413342 13 38171301 38171312 POSTN 0.000413642 19 7995974 7996007 TIMM44 0.000414721 10 12226870 12226882 NUDT5 0.000415483 6 109480681 109480693 CEP57L1 0.000416475 X 135328309 135328320 MAP7D3 0.000417679 5 137513369 137513382 BRD8 0.000417833 3 33893929 33893949 PDCD6IP 0.000423268 1 237060945 237060970 MTR 0.000427426 3 10429902 10429913 ATP2B2 0.000428436 1 92944314 92944351 GFI1 0.000430436 6 131948469 131948501 MED23 0.000431417 3 32933344 32933365 TRIM71 0.000431546 14 64460536 64460551 SYNE2 0.000432367 7 73279233 73279260 WBSCR28 0.000432896 2 191941054 191941078 STAT4 0.000433708 4 151835502 151835539 LRBA 0.000440614 3 194159705 194159736 ATP13A3 0.000442086 5 60982634 60982645 LOC101928651 0.000444366 1 207679180 207679198 CR1 0.00044455 12 21639385 21639398 RECQL 0.000446918 16 20803249 20803265 ACSM3, ERI2 0.000450863 5 115628120 115628134 COMMD10 0.00045249 1 33087567 33087584 ZBTB8OS 0.000455645 11 65647789 65647810 CTSW 0.000455868 15 52239617 52239629 LEO1 0.000459931 7 36465606 36465622 ANLN 0.000460705 15 41770639 41770652 RTF1 0.000460705 16 90141288 90141302 PRDM7 0.000465942 7 150918586 150918602 ABCF2 0.00046677 5 126866119 126866130 PRRC1 0.000467188 14 53513439 53513452 DDHD1 0.000478649 14 93712634 93712660 BTBD7 0.000479866 10 69716602 69716614 HERC4 0.000481752 8 21846488 21846505 XPO7 0.000484079 20 35632021 35632042 RBL1 0.000488807 11 118883880 118883892 CCDC84 0.000490191 17 27829588 27829602 TAOK1 0.000493431 19 54264352 54264364 MIR516A2 0.000495727 18 31523144 31523156 NOL4 0.000496542 4 10027509 10027520 SLC2A9 0.000497979 1 215345245 215345313 KCNK2 0.000499439 6 144758647 144758660 UTRN 0.000499476 4 57686807 57686822 SPINK2 0.000503914 2 102785158 102785171 IL1R1 0.000511534 2 32427092 32427104 SLC30A6 0.000513291 4 169190129 169190143 DDX60 0.000514018 X 135053121 135053154 MMGT1 0.000515531 10 123310733 123310744 FGFR2 0.000518238 6 38905667 38905680 LOC100131047 0.000519154 18 43445730 43445748 EPG5 0.000521147 2 47635523 47635537 MSH2 0.000521166 1 33799658 33799669 PHC2 0.000522835 7 92883250 92883261 CCDC132 0.000524287 6 47567210 47567222 CD2AP 0.000524605 12 10205420 10205435 CLEC9A 0.000526676 X 44949951 44949963 KDM6A 0.000529903 15 30406088 30406103 ULK4P3 0.000533847 1 150676674 150676692 HORMAD1 0.000535678 1 74575199 74575231 LRRIQ3 0.000536674 10 114154662 114154673 ACSL5 0.000540155 X 83403148 83403160 RPS6KA6 0.00054065 5 140812775 140812788 PCDHGA12 0.000540991 19 55444906 55444921 NLRP7 0.00054188 10 12240681 12240702 CDC123 0.000541893 21 38498341 38498356 TTC3 0.000541948 15 63040516 63040533 TLN2 0.000545158 1 210411266 210411281 SERTAD4 0.000545366 9 102730697 102730712 STX17 0.00055051 7 106888946 106888972 COG5 0.000550939 3 113377481 113377493 KIAA2018 0.000553112 7 135099044 135099059 CNOT4 0.000553432 1 109773427 109773451 SARS 0.000553805 9 130413851 130413880 STXBP1 0.00055571 11 35287000 35287014 SLC1A2 0.000560024 2 228680153 228680168 CCL20 0.000564239 1 154112163 154112180 NUP210L 0.00056524 6 110426583 110426595 WASF1 0.000567544 11 124624705 124624721 ESAM 0.000571783 15 86279430 86279457 AKAP13 0.000573655 6 123545159 123545186 TRDN 0.000585494 12 30822226 30822240 IPO8 0.000587147 15 23333801 23333815 HERC2P2 0.000588027 1 32631598 32631676 KPNA6 0.000589911 11 22296094 22296106 ANO5 0.000591354 9 84267021 84267054 TLE1 0.000592855 6 119501609 119501620 MAN1A1 0.000594016 11 47840864 47840879 NUP160 0.000594717 4 167020771 167020795 TLL1 0.000597441 12 13364426 13364437 EMP1 0.000597661 12 56744020 56744045 STAT2 0.000599413 X 24745018 24745047 POLA1 0.000600192 6 24412431 24412445 MRS2 0.000608675 3 186522293 186522308 RFC4 0.000609401 2 120712718 120712731 PTPN4 0.000609401 12 27841925 27841938 PPFIBP1 0.000609509 12 27877126 27877148 MRPS35 0.000610049 2 91887905 91887919 LOC654342(dist = 39930), 0.000610207 GGT8P(dist = 75449) 12 99059316 99059327 APAF1 0.000610207 12 45771901 45771918 ANO6 0.000610833 X 22244528 22244549 PHEX 0.000615633 20 23473522 23473535 CST8 0.000622379 2 61187478 61187496 PUS10 0.000635196 19 12128923 12128937 ZNF433 0.000635849 7 151884279 151884292 KMT2C 0.000636802 22 30051705 30051722 NF2 0.000637223 15 73418741 73418756 NEO1 0.000638666 6 90366329 90366347 LOC101929057 0.000645585 5 70848879 70848890 BDP1 0.000648316 1 155884155 155884167 KIAA0907 0.000648654 3 107910327 107910342 IFT57 0.000649415 8 17422434 17422446 SLC7A2 0.000651271 1 98011812 98011842 DPYD 0.000662468 2 61577667 61577680 USP34 0.000663347 4 119666217 119666241 SEC24D 0.000663806 2 48033875 48033909 MSH6 0.000668448 2 169994021 169994058 LRP2 0.000671582 1 234565078 234565090 TARBP1 0.00067177 22 32548036 32548047 C22orf42 0.000671841 2 179442292 179442314 MIR548N, TTN-AS1 0.000671892 2 152589615 152589626 NEB 0.000675485 16 3828847 3828870 CREBBP 0.000679186 12 56380950 56380964 RAB5B 0.000681492 X 19086800 19086823 GPR64 0.000681492 2 157370018 157370033 GPD2 0.000681993 12 131476665 131476692 GPR133 0.00068284 6 18258299 18258311 DEK 0.000693505 1 144916415 144916426 NBPF20, NBPF9, PDE4DIP 0.000695925 4 25160732 25160748 SEPSECS 0.000697507 15 50152754 50152776 ATP8B4 0.000698812 2 101581294 101581308 NPAS2 0.000704355 1 52403174 52403187 RAB3B 0.000704639 6 158049351 158049365 ZDHHC14 0.000707336 4 41015553 41015566 APBB2 0.000708852 7 6771663 6771684 ZNF12(dist = 25097), 0.00071122 PMS2CL(dist = 3252) 14 76173952 76173964 TTLL5 0.000712406 11 125763610 125763624 PUS3 0.000716302 1 231094050 231094067 TTC13 0.000718986 3 190338028 190338060 IL1RAP 0.000720894 2 191155233 191155245 HIBCH 0.000730721 3 143235916 143235929 SLC9A9 0.000732601 7 77797468 77797490 MAGI2 0.000732859 1 183498191 183498202 SMG7 0.000735791 19 21428062 21428087 ZNF431(dist = 59257), 0.000736402 ZNF708(dist = 45875) 17 7726648 7726698 DNAH2 0.000744655 1 9192336 9192365 DENND5A 0.00075596 2 68772281 68772292 APLF 0.000757479 6 88221097 88221109 SLC35A1 0.000761518 16 15162143 15162165 PDXDC1, RRN3 0.000766289 21 37706087 37706100 MORC3 0.000768534 5 108516618 108516640 FER 0.000772105 17 29563068 29563089 NF1 0.0007733 18 33058318 33058335 INO80C 0.000776871 11 132179950 132179979 NTM 0.00077799 17 35988718 35988739 DDX52 0.000780376 13 37596114 37596125 SUPT20H 0.000781111 8 124244005 124244016 C8orf76, ZHX1-C8orf76 0.000784314 11 121367557 121367571 SORL1 0.000787353 X 15364158 15364186 PIR-FIGF 0.000787738

TABLE 15 Microsatellite Repeat Marker Sequences for Ovarian Serous Cystadenocarcinoma (OV). TABLE 15 - OV ch start_pos end_pos (hg37) (hg37) (hg37) gene OV p-value 7 23761159 23761171 STK31 0.000138358 3 9102112 9102129 SRGAP3 0.000154596 17 52991026 52991047 TOM1L1 0.000164836 X 135115669 135115681 SLC9A6 0.000306057 8 100287517 100287536 VPS13B 0.000388149 1 74818936 74818947 FPGT-TNNI3K, TNNI3K 0.000510827 12 64891393 64891418 TBK1 0.000580495 10 88458996 88459025 LDB3 0.00079249 7 104309164 104309177 LHFPL3 0.001077249 1 206566852 206566872 SRGAP2D 0.00112585 X 131231430 131231468 FRMD7 0.001292105 15 65273147 65273161 SPG21 0.0013328 12 124116817 124116847 EIF2B1 0.001966955 1 158224559 158224624 CD1A 0.002282105 15 34654339 34654358 LPCAT4 0.002298213 20 42199704 42199743 SGK2 0.002363852 1 176105710 176105723 RFWD2 0.002407981 6 49415351 49415368 MUT 0.002510486 11 14063262 14063275 SPON1 0.002583661 18 6975847 6975857 LAMA1 0.002633889 1 79383748 79383762 ELTD1 0.002877698 8 7191539 7191558 FAM66B 0.002912056 9 128064242 128064260 GAPVD1 0.002939735 12 109701959 109701975 ACACB 0.003011318 12 49091972 49092009 CCNT1 0.00329608 1 46650191 46650201 TSPAN1 0.003361142 17 18708830 18708843 TVP23B 0.003661465 17 61898129 61898142 FTSJ3 0.003830439 6 111702448 111702460 REV3L 0.004010111 2 131888361 131888376 PLEKHB2 0.004016064 10 64022582 64022593 RTKN2 0.004262575 8 65528842 65528854 CYP7B1 0.004516712 1 113657018 113657033 LRIG2 0.004645161 6 7413094 7413107 RIOK1 0.004856512 7 91509436 91509457 MTERF1 0.004897959 1 173795803 173795821 DARS2 0.005042017 1 207753824 207753846 CR1 0.005128205 12 16052767 16052780 STRAP 0.005366726 12 107398862 107398876 CRY1 0.005367724 5 94842718 94842730 TTC37 0.005589194 1 220369745 220369758 RAB3GAP2 0.005664965 1 201832479 201832492 IPO9 0.005734543 X 21534510 21534521 CNKSR2 0.005797101 3 107910327 107910342 IFT57 0.005865422 2 87049358 87049371 CD8B 0.005961252 15 35083508 35083555 LOC101928174 0.006058371 X 122598635 122598648 GRIA3 0.006143242 2 21226218 21226230 APOB 0.006265664 2 136690414 136690443 DARS 0.006303735 7 33075634 33075645 NT5C3A 0.006342495 12 55354876 55354889 TESPA1 0.006518905 16 15501658 15501670 MPV17L 0.00669203 1 58380192 58380205 ZFP91-CNTF 0.006714213 16 81051115 81051128 CENPN 0.006858499 1 211280724 211280748 KCNH1 0.007211241 14 24571860 24571874 PCK2 0.007510446 2 236706612 236706623 AGAP1 0.007519945 19 22585521 22585535 ZNF98 0.007611165 X 21544904 21544935 CNKSR2 0.007692308 1 175087683 175087694 TNN 0.007747087 22 42415224 42415240 WBP2NL 0.007784946 11 59368218 59368235 OSBP 0.00784744 4 17964528 17964539 LCORL 0.008097166 5 68413042 68413072 SLC30A5 0.008206581 5 68396764 68396793 SLC30A5 0.008764684 7 33192288 33192300 BBS9 0.008766803 19 6026288 6026302 RFX2 0.008885851 X 1467519 1467589 IL3RA 0.009114066 11 58892376 58892387 FAM111B 0.009324009 13 20325367 20325378 PSPC1 0.009398496 2 103281540 103281552 SLC9A2 0.009484187 19 56329186 56329204 NLRP11 0.00966544 6 84649715 84649747 CYB5R4 0.00970483 14 103192774 103192791 RCOR1 0.009886234 14 51477220 51477231 TRIM9 0.01 17 35567303 35567314 ACACA 0.010486231 17 54981571 54981588 TRIM25 0.010512345 5 50122645 50122660 PARP8 0.01072434 20 18505555 18505576 SEC23B 0.01072434 17 53014442 53014457 TOM1L1 0.010755482 14 81574687 81574712 TSHR 0.010977266 13 50586051 50586064 DLEU2 0.011144436 15 86188984 86189019 AKAP13 0.011177158 14 52981552 52981563 TXNDC16 0.011310323 12 94818770 94818802 CEP83 0.011378114 X 44949951 44949963 KDM6A 0.011471034 10 45984725 45984740 MARCH8 0.011555078 8 28707622 28707636 INTS9 0.011645202 14 21936762 21936776 RAB2B 0.011656661 6 116914112 116914128 RWDD1 0.011724301 X 2343183 2343213 DHRSX 0.011904684 15 41350749 41350793 INO80 0.01209145 6 152631788 152631821 SYNE1 0.012200061 4 113107829 113107845 C4orf32 0.012294372 5 61745737 61745750 IPO11 0.012337984 2 63182611 63182622 EHBP1 0.012479102 2 9552383 9552396 ITGB1BP1 0.012575687 2 56611386 56611398 CCDC85A 0.012663953 16 4873743 4873761 GLYR1 0.012691424 2 136511898 136511910 UBXN4 0.012720908 14 50605267 50605280 SOS2 0.013151028 12 95488339 95488354 FGD6 0.013547775 6 105405900 105405913 LIN28B 0.013888889 2 211457713 211457724 CPS1 0.013888889 9 86920104 86920135 SLC28A3 0.014739765 8 95507237 95507250 KIAA1429 0.014787155 7 106888946 106888972 COG5 0.01509952 7 102825987 102826001 DPY19L2P2 0.015242366 1 29476535 29476555 SRSF4 0.015625 12 56744020 56744045 STAT2 0.015961596 7 152144203 152144216 FABP5P3(dist = 4103), LINC01003(dist = 16993) 0.016069586 15 50581627 50581647 GABPB1 0.016129032 2 119739127 119739142 MARCO 0.016278948 2 43778857 43778869 THADA 0.016574113 6 80837242 80837253 BCKDHB 0.016579523 5 41909830 41909846 5orf5 0.016637417 5 33546113 33546143 ADAMTS12 0.016947811 13 77792099 77792113 MYCBP2 0.017281606 9 85597720 85597749 RASEF 0.017337643 21 17238572 17238582 USP25 0.017500648 1 38052867 38052907 GNL2 0.0178959 20 10622080 10622091 JAG1 0.018087462 7 18688019 18688056 HDAC9 0.018103117 3 130660392 130660405 ATP2C1 0.018365415 1 248524799 248524818 OR2T4 0.018731926 17 71223424 71223438 FAM104A 0.018918799 X 110494528 110494543 CAPN6 0.019645318 10 26825151 26825168 APBB1IP 0.019718823 1 158584103 158584116 SPTA1 0.019822501 12 88926290 88926302 KITLG 0.019961408 9 117783551 117783586 TNC 0.020082879 1 36888302 36888316 OSCP1 0.020260267 17 4646533 4646547 ZMYND15 0.020449216 7 20180507 20180526 MACC1(NM_182762: c.*62_43del0) 0.020578912 1 47325299 47325313 CYP4Z2P 0.020804132 12 22063251 22063266 ABCC9 0.020909254 6 51910735 51910747 PKHD1 0.021012212 6 36483295 36483334 STK38 0.021307895 X 133511862 133511890 PHF6 0.02158136 1 169797067 169797078 C1orf112 0.02173913 3 124998098 124998118 ZNF148 0.022213678 19 20317771 20317824 ZNF486(dist = 6472), MIR1270(dist = 192257) 0.022222222 10 90362299 90362324 LIPJ 0.022555223 15 98513086 98513103 ARRDC4 0.023165075 16 57249981 57250000 RSPRY1 0.023343584 X 77264514 77264533 ATP7A 0.023724164 18 56245965 56246014 ALPK2 0.023834984 17 31266427 31266441 TMEM98 0.024691358 14 93686568 93686587 UBR7 0.025385559 17 10317164 10317176 MYHAS 0.02540136 5 142601811 142601862 ARHGAP26 0.025725356 5 83550060 83550071 EDIL3 0.0258581 20 480602 480627 CSNK2A1 0.026556271 X 123204978 123204993 STAG2 0.02673838 6 33408890 33408917 SYNGAP1 0.026771921 16 89576879 89576895 SPG7 0.026923077 11 61977858 61977881 SCGB2A1 0.027878415 10 17279211 17279223 VIM 0.028169014 7 102038153 102038199 LOC100630923 0.0282742 19 44662274 44662288 ZNF234(NM_006630: c.*2_*16del0, 0.028565004 NM_001144824: c.*2_*16del0) 8 131193153 131193166 ASAP1 0.028604681 13 42772765 42772789 DGKH 0.029332546 2 215876589 215876603 ABCA12 0.029371838 10 134628521 134628532 CFAP46 0.029411765 15 44216559 44216573 FRMD5 0.029913113 17 33318204 33318216 LIG3 0.03030303 11 89395303 89395315 FOLH1B 0.030808872 17 30293149 30293164 SUZ12 0.03125 1 200559220 200559231 KIF14 0.03125 3 62153593 62153621 PTPRG 0.031265558 9 99408079 99408094 AAED1 0.031298797 8 24253166 24253199 LOC101929294 0.031464833 1 29016705 29016737 GMEB1 0.031496063 6 148761410 148761421 SASH1 0.031736765 11 125488247 125488261 STT3A 0.031746032 1 3117272 3117311 IL32 0.032126697 3 160141137 160141173 SMC4 0.032258065 2 234178624 234178640 ATG16L1 0.032487998 14 20666587 20666598 OR11G2 0.03249381 6 144814625 144814664 UTRN 0.032967033 2 47702411 47702471 MSH2 0.033057851 12 104515109 104515121 NFYB 0.033333333 10 32099547 32099559 ARHGAP12 0.033421118 12 131476665 131476692 GPR133 0.033464212 5 135496820 135496834 SMAD5 0.033740307 1 16354441 16354448 CLCNKA 0.034002981 2 225035745 225035758 SERPINE2(dist = 131709), FAM124B(dist = 207657) 0.034782609 2 139308383 139308420 SPOPL 0.034836366 13 32907535 32907547 BRCA2 0.034965035 16 47399670 47399687 ITFG1 0.035255751 7 92900502 92900527 CCDC132 0.035294118 11 14539315 14539332 PSMA1 0.03536144 10 43671378 43671392 CSGALNACT2 0.03536144 1 66829000 66829011 PDE4B 0.035714286 14 51062236 51062290 ATL1 0.036136806 8 110334770 110334782 NUDCD1 0.036363636 19 9771286 9771300 ZNF562 0.036641489 17 45992566 45992604 SP2-AS1 0.037003666 17 57278908 57278920 PRR11 0.037037037 4 143181722 143181748 INPP4B 0.037037037 11 101362164 101362178 TRPC6 0.037096174 16 69385403 69385421 TMED6 0.037313433 4 54327211 54327223 LNX1 0.037405047 7 26247984 26247997 CBX3 0.0375 6 134210497 134210516 TCF21(NM_198392: c.-39_-20del-, 0.037553034 NM_003206: c.-39_-20del-) 3 38137959 38137970 DLEC1 0.037878788 2 39240584 39240596 SOS1 0.038167939 12 114837219 114837235 TBX5 0.038228009 1 74901739 74901760 FPGT-TNNI3K, TNNI3K 0.038250334 2 69420574 69420634 ANTXR1 0.038461538 20 9360821 9360845 PLCB4 0.038461538 13 50098426 50098438 PHF11 0.038461538 9 104306988 104307005 RNF20 0.038834951 14 60587879 60587900 PCNXL4 0.038944472 3 67058329 67058357 KBTBD8 0.039215686 10 25273311 25273328 ENKUR 0.039370079 12 110834030 110834049 ANAPC7 0.03968254 1 218578726 218578745 TGFB2 0.03979798 8 90933269 90933296 OSGIN2 0.04 1 184692999 184693020 EDEM3 0.040197897 X 129265852 129265866 AIFM1 0.040268456 1 155631307 155631342 YY1AP1 0.040342941 6 117026217 117026229 KPNA5 0.04040404 14 45696752 45696769 MIS18BP1 0.040677344 9 123945492 123945515 RAB14 0.040677344 19 45781081 45781156 MARK4 0.040873436 19 55452749 55452775 NLRP7 0.041237113 10 6273170 6273182 PFKFB3 0.04131008 22 26769464 26769477 SEZ6L 0.041411937 2 80101515 80101528 CTNNA2 0.041428455 6 154489255 154489267 IPCEF1, OPRM1 0.041648418 9 30689085 30689104 LINC01242(dist = 280633), ACO1(dist = 1695497) 0.041666667 10 116605738 116605750 FAM160B1 0.041666667 1 28785729 28785740 PHACTR4 0.041666667 5 67576330 67576346 PIK3R1 0.041666667 15 34553225 34553236 SLC12A6 0.041666667 21 44513110 44513140 U2AF1(NM_001025204: c.*102_*72del0, 0.042016807 NM_006758: c.*102_*72del0, NM_001025203: c.*102_*72del0) 12 27877126 27877148 MRPS35 0.042253521 1 186089102 186089113 MIR548F1 0.042253521 20 36431202 36431215 CTNNBL1 0.042253521 7 20180425 20180476 MACC1(NM_182762: c.*144_*93del0) 0.042263434 16 19619602 19619617 C16orf62 0.042403642 5 16764255 16764277 MYO10 0.042421256 2 64139831 64139844 VPS54 0.042553191 12 64491002 64491019 SRGAP1 0.042735043 13 73636910 73636929 KLF5 0.042778962 9 33062183 33062195 SMU1 0.042855001 4 7780663 7780674 AFAP1 0.042857143 8 82583104 82583133 IMPA1 0.042857143 4 141484371 141484383 UCP1 0.042933022 2 170413815 170413834 FASTKD1 0.042944785 10 105139888 105139903 TAF5 0.043165468 13 43491778 43491796 EPSTI1 0.043315982 12 132539500 132539513 EP400 0.043478261 5 112903585 112903598 YTHDC2 0.043478261 2 84668258 84668269 SUCLG1 0.043478261 9 19334957 19334970 DENND4C 0.044025157 13 21729952 21729979 SKA3 0.044040367 14 73079138 73079150 RGS6(dist = 45900), DPF3(dist = 6854) 0.044247788 20 47268978 47268996 PREX1 0.044247788 15 43720155 43720172 RNU6-28P 0.044405603 17 73515055 73515068 TSEN54 0.044585987 X 119675354 119675368 CUL4B 0.044585987 11 47187055 47187087 ARFGAP2 0.044871795 1 11134470 11134485 EXOSC10 0.044871795 11 57472141 57472167 MED19 0.045045045 10 93695545 93695556 BTAF1 0.045454545 16 31196218 31196237 FUS 0.045454545 7 95775848 95775863 SLC25A13 0.045454545 15 53815527 53815550 WDR72 0.045612905 8 89128708 89128722 MMP16 0.045893255 2 192225477 192225514 MYO1B 0.045961358 1 214825289 214825312 CENPF 0.046052632 9 69127139 69127155 PGM5P2 0.046073819 15 55972660 55972674 PRTG 0.046113395 20 4839890 4839911 SLC23A2 0.046357616 7 142139624 142139663 TRY2P(dist = 167556), MTRNR2L6(dist = 234468) 0.046357616 7 77006092 77006113 GSAP 0.046511628 16 28842257 28842275 ATXN2L 0.047169811 17 72285659 72285679 DNAI2 0.047463312 20 33225781 33225808 PIGU 0.047619048 15 81187286 81187297 CEMIP 0.047619048 5 54701447 54701491 SKIV2L2 0.047619048 5 74097328 74097361 FAM169A 0.047619048 12 6657402 6657417 IFFO1 0.047619048 2 157370018 157370033 GPD2 0.047904192 7 16704933 16704945 BZW2 0.048076923 13 99890849 99890862 MIR548AN 0.048192771 18 319944 319956 COLEC12(NM_130386: c.*101_*89del0) 0.048275862 X 36156447 36156461 CHDC2 0.048354085 11 32852019 32852043 PRRG4 0.048387097 1 62740780 62740792 KANK4 0.048611111 4 115586972 115586988 UGT8 0.048780488 13 110833751 110833764 COL4A1 0.048780488 4 183600752 183600764 TENM3 0.048803828 18 12955439 12955452 SEH1L 0.048979213 3 71739332 71739345 EIF4E3 0.049079755 X 54042926 54042942 PHF8 0.049180328 1 28218773 28218784 RPA2 0.049180328 6 90503754 90503779 MDN1 0.049180328 6 42611936 42611951 UBR2 0.049295775 X 22244528 22244549 PHEX 0.049484117 3 7494245 7494274 GRM7 0.049558489 9 134049353 134049366 NUP214 0.049586777 2 131883287 131883301 PLEKHB2 0.049586777 14 67848479 67848493 EIF2S1 0.049586777 20 33665775 33665786 TRPC4AP 0.04964539 16 7743418 7743437 RBFOX1 0.049723757 11 16117460 16117478 SOX6 0.05 14 75508258 75508303 MLH3 0.05 X 117530912 117530925 WDR44 0.05 14 75476004 75476015 EIF2B2(NM_014239: c.*113_*124del0) 0.05

Definitions

Unless otherwise defined herein, scientific and technical terms used in connection with the present application shall have the meanings that are commonly understood by those of ordinary skill in the art to which this disclosure belongs. It should be understood that this invention is not limited to the particular methodology, protocols, and reagents, etc., described herein and as such can vary. The terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention, which is defined solely by the claims. Definitions of common terms in cell biology, immunology and molecular biology can be found in The Merck Manual of Diagnosis and Therapy, 20th Edition, published by Merck Sharp & Dohme Corp., 2018 (ISBN 0911910190, 978-0911910421); Robert S. Porter et al. (eds.), The Encyclopedia of Molecular Cell Biology and Molecular Medicine, published by Blackwell Science Ltd., 1999-2012 (ISBN 9783527600908); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8); Immunology by Werner Luttmann, published by Elsevier, 2006; Janeway's Immunobiology, Kenneth Murphy, Allan Mowat, Casey Weaver (eds.), W. W. Norton & Company, 2016 (ISBN 0815345054, 978-0815345053); Lewin's Genes XI, published by Jones & Bartlett Publishers, 2014 (ISBN-1449659055); Michael Richard Green and Joseph Sambrook, Molecular Cloning: A Laboratory Manual, 4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (2012) (ISBN 1936113414); Davis et al., Basic Methods in Molecular Biology, Elsevier Science Publishing, Inc., New York, USA (2012) (ISBN 044460149X); Laboratory Methods in Enzymology: DNA, Jon Lorsch (ed.) Elsevier, 2013 (ISBN 0124199542); Current Protocols in Molecular Biology (CPMB), Frederick M. Ausubel (ed.), John Wiley and Sons, 2014 (ISBN 047150338X, 9780471503385), Current Protocols in Protein Science (CPPS), John E. Coligan (ed.), John Wiley and Sons, Inc., 2005; and Current Protocols in Immunology (CPI) (John E. Coligan, ADA M Kruisbeek, David H Margulies, Ethan M Shevach, Warren Strobe, (eds.) John Wiley and Sons, Inc., 2003 (ISBN 0471142735, 9780471142737), the contents of which are all incorporated by reference herein in their entireties.

For convenience, the meaning of some terms and phrases used in the specification, examples, and appended claims, are provided below. Unless stated otherwise, or implicit from context, the following terms and phrases include the meanings provided below. The definitions are provided to aid in describing particular embodiments, and are not intended to limit the claimed invention, because the scope of the invention is limited only by the claims. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. If there is an apparent discrepancy between the usage of a term in the art and its definition provided herein, the definition provided within the specification shall prevail.

An “agent” can be any chemical, entity or moiety, including without limitation synthetic and naturally-occurring proteinaceous and non-proteinaceous entities. In some embodiments, an agent is a nucleic acid, nucleic acid analog, protein, antibody, peptide, aptamer, oligomer of nucleic acids, amino acids, or carbohydrates including without limitation a protein, oligonucleotide, ribozyme, DNAzyme, glycoprotein, siRNAs, lipoprotein and/or a modification or combinations thereof etc. In certain embodiments, agents are small molecule chemical moieties. For example, chemical moieties included unsubstituted or substituted alkyl, aromatic, or heterocyclyl moieties including macrolides, leptomycins and related natural products or analogues thereof. Compounds can be known to have a desired activity and/or property, or can be selected from a library of diverse compounds.

An agent can be a molecule from one or more chemical classes, e.g., organic molecules, which may include organometallic molecules, inorganic molecules, genetic sequences, etc. Agents may also be fusion proteins from one or more proteins, chimeric proteins (for example domain switching or homologous recombination of functionally significant regions of related or different molecules), synthetic proteins or other protein variations including substitutions, deletions, insertions and other variants.

The term “therapeutically effective amount” refers to an amount of a therapeutic as described herein, that is effective to treat a disease or disorder as the terms “treat” or “treatment” are defined herein. Amounts will vary depending on the specific disease or disorder, its state of progression, age, weight and gender of a subject, among other variables. Thus, it is not possible to specify an exact “effective amount”. However, for any given case, an appropriate “effective amount” can be determined by one of ordinary skill in the art using only routine experimentation.

As used herein, the term “checkpoint inhibitor immunotherapy” refers to any agent, small molecule, antibody, or the like that can reduce or inhibit the level or activity of an immune checkpoint molecule. Inhibition of an immune checkpoint molecule can promote an immune response, e.g., against cancer or a tumor which otherwise evades such response. Immune checkpoint molecules can include but are not limited to PD-1 or PD-L1, CTLA4, Adenosine A2A receptor (A2AR), CD276, CD39, CD73, B7 family immune checkpoint molecules, V-set domain-containing T-cell activation inhibitor 1 (B7H4), B and T Lymphocyte Attenuator (BTLA), Indoleamine 2,3-dioxygenase (IDO), Killer-cell Immunoglobulin-like Receptor (KIR), Lymphocyte Activation Gene-3 (LAG3), nicotinamide adenine dinucleotide phosphate NADPH oxidase isoform 2 (NOX2), T-cell Immunoglobulin domain and Mucin domain 3 (TIM-3), T cell immunoreceptor with Ig and ITIM domains (TIGIT), V-domain Ig suppressor of T cell activation (VISTA), and Sialic acid-binding immunoglobulin-type lectin 7 (SIGLEC7), and those described, e.g., Pardoll et al., Nature Reviews Cancer 12, 252-264 (2012), which is incorporated herein by reference in its entirety. Non-limiting examples of checkpoint inhibitors include pembrolizumab (Keytruda®), nivolumab (Opdivo®), cemiplimab (Libtayo®), spartalizumab, camrelizumab, sintilimab, tislelizumab, toripalimab, dostarlimab, INVMGA00012, AMP-224, AMP-514, atezolizumab (Tecentriq®), avelumab (Bavencio®), survalumab (Imfinzi®), KN035, CK-301, AUNP12, CA-170, BMS-986189, and ipilimumab (Yervoy®)

As used herein, the term “non-checkpoint inhibitor cancer therapy” refers to any therapy or agent useful in treating cancer other than checkpoint inhibitor immunotherapy. One of skill in the art can readily identify a non-checkpoint inhibitor chemotherapeutic agent, e.g. see Physicians' Cancer Chemotherapy Drug Manual 2014, Edward Chu, Vincent T. DeVita Jr., Jones & Bartlett Learning; Principles of Cancer Therapy, Chapter 85 in Harrison's Principles of Internal Medicine, 18th edition; Therapeutic Targeting of Cancer Cells: Era of Molecularly Targeted Agents and Cancer Pharmacology, Chs. 28-29 in Abeloff's Clinical Oncology, 2013 Elsevier; Baltzer L, Berkery R (eds): Oncology Pocket Guide to Chemotherapy, 2nd ed. St. Louis, Mosby-Year Book, 1995; Fischer D S (ed): The Cancer Chemotherapy Handbook, 4th ed. St. Louis, Mosby-Year Book, 2003)).

As used herein, the term “cancer” refers to a hyperproliferation of cells that exhibit a loss of normal cellular control that results in unregulated growth, lack of differentiation, local tissue invasion, and metastasis. Non-limiting examples of cancer types include, but are not limited to, human sarcomas and carcinomas, e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, colorectal cancer, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, liver cancer, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, cervical cancer, bone cancer, brain tumor, testicular cancer, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma, melanoma, neuroblastoma, retinoblastoma; leukemias, e.g., acute lymphocytic leukemia and acute myelocytic leukemia (myeloblastic, promyelocytic, myelomonocytic, monocytic and erythroleukemia); chronic leukemia (chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia); and polycythemia vera, lymphoma (Hodgkin's disease and non-Hodgkin's disease), multiple myeloma, Waldenstrom's macroglobulinemia, heavy chain disease. In some embodiments of any of the aspects, the cancer type is selected from the group consisting of: BLCA, Bladder Urothelial Carcinoma; BRCA, Breast invasive carcinoma; CESC, Cervical squamous cell carcinoma and endocervical adenocarcinoma; CHOL, Cholangiocarcinoma; COAD, Colon adenocarcinoma; DLBC, Lymphoid Neoplasm Diffuse Large B-cell Lymphoma; ESCA, Esophageal carcinoma; GBM, Glioblastoma multiforme; HNSC, Head and Neck squamous cell carcinoma; KICH, Kidney Chromophobe; KIRC, Kidney renal clear cell carcinoma; KIRP, Kidney renal papillary cell carcinoma; LAML, Acute Myeloid Leukemia; LGG, Brain Lower Grade Glioma; LIHC, Liver hepatocellular carcinoma; LUAD, Lung adenocarcinoma; LUSC, Lung squamous cell carcinoma; MESO, Mesothelioma; OV, Ovarian serous cystadenocarcinoma; PAAD, Pancreatic adenocarcinoma; PCPG, Pheochromocytoma and Paraganglioma; PRAD, Prostate adenocarcinoma; READ, Rectum adenocarcinoma; SARC, Sarcoma; SKCM, Skin Cutaneous Melanoma; STAD, Stomach adenocarcinoma; TGCT, Testicular Germ Cell Tumors; THCA, Thyroid carcinoma; THYM, Thymoma; UCEC, Uterine Corpus Endometrial Carcinoma; UCS, Uterine Carcinosarcoma; and UVM, Uveal Melanoma.

As used herein the term “microsatellite instability” or “MSI” refers to a molecular tumor phenotype that is indicative of genomic hypermutability, marked by spontaneous gains or losses of nucleotides from repetitive DNA tracts, resulting in new alleles of differing length.

As used herein, the term “microsatellite repeat sequence” refers to a repetitive nucleotide sequence of about 1-6 base pairs or more in length. The repeat sequences can vary in number of repeats, generally ranging from about 5 to about 60 repeats. The methods provided herein are based, in part, on microsatellite mutations relative to microsatellite repeat sequences in the reference human genome, GRCh37/hg19. A microsatellite repeat sequence can be identified, for example, using tools such as the microsatellite identification tool (MISA), found on the world wide web at <webblast.ipk-gatersleben.de/misa/>.

As used herein, the terms “treat,” “treatment,” “treating,” or “amelioration” refer to therapeutic treatments, wherein the object is to reverse, alleviate, ameliorate, inhibit, slow down or stop the progression or severity of a condition associated with, a disease or disorder. The term “treating” includes reducing or alleviating at least one adverse effect or symptom of a disease or disorder. Treatment is generally “effective” if one or more symptoms or clinical markers are reduced. Alternatively, treatment is “effective” if the progression of a disease is reduced or halted. That is, “treatment” includes not just the improvement of symptoms or markers, but also a cessation of at least slowing of progress or worsening of symptoms that would be expected in absence of treatment. Beneficial or desired clinical results include, but are not limited to, alleviation of one or more symptom(s), diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total). The term “treatment” of a disease also includes providing relief from the symptoms or side-effects of the disease (including palliative treatment).

The terms “decrease”, “reduce”, “reduction”, or “inhibit” are all used herein to mean a decrease by a statistically significant amount. In some embodiments, “reduce,” “reduction”, “decrease” or “inhibit” means a decrease by at least 10% as compared to a reference level (e.g. the absence of a given treatment) and can include, for example, a decrease by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, at least about 99%, or more. As used herein, “reduction” or “inhibition” does not encompass complete inhibition or reduction as compared to a reference level. “Complete inhibition” is a 100% inhibition as compared to a reference level.

The terms “increased”, “increase”, “enhance”, or “activate” are all used herein to mean an increase by a statically significant amount. In some embodiments, the terms “increased”, “increase”, “enhance”, or “activate” can mean an increase of at least 10% as compared to a reference level, for example an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% increase or any increase between 10-100% as compared to a reference level, or at least about a 2-fold, or at least about a 3-fold, or at least about a 4-fold, or at least about a 5-fold or at least about a 10-fold increase, or any increase between 2-fold and 10-fold or greater as compared to a reference level.

As used herein, a “subject” is a human or a non-human animal. Usually the non-human animal is a vertebrate such as a primate, rodent, domestic animal or game animal. Primates include chimpanzees, cynomolgus monkeys, spider monkeys, and macaques, e.g., Rhesus. Rodents include mice, rats, woodchucks, ferrets, rabbits and hamsters. Domestic and game animals include cows, horses, pigs, deer, bison, buffalo, feline species, e.g., domestic cat, canine species, e.g., dog, fox, wolf, avian species, e.g., chicken, emu, ostrich, and fish, e.g., trout, catfish and salmon. In some embodiments, the subject is a mammal, e.g., a primate, e.g., a human. The terms, “individual,” “patient” and “subject” are used interchangeably herein.

Preferably, the subject is a mammal. The mammal can be a human, non-human primate, mouse, rat, dog, cat, horse, or cow, but is not limited to these examples. Mammals other than humans can be advantageously used as subjects that represent animal models of diseases including diseases and disorders involving inappropriate immunosuppression. A subject can be male or female.

A subject can be one who has been previously diagnosed with or identified as suffering from or having a condition in need of treatment or one or more complications related to such a condition, and optionally, have already undergone treatment for the condition or the one or more complications related to the condition. Alternatively, a subject can also be one who has not been previously diagnosed as having the condition or one or more complications related to the condition. For example, a subject can be one who exhibits one or more risk factors for the condition or one or more complications related to the condition or a subject who does not exhibit risk factors.

As used herein, a “subject in need” of treatment for a particular condition can be a subject having that condition, diagnosed as having that condition, or at risk of developing that condition. In one embodiment, a subject in need either has the condition or has been diagnosed as having the condition.

As used herein, a “reference level” refers to the level of a given, e.g., biomarker or parameter useful as a gauge for an experimental or diagnostic measurement. In one embodiment, a reference level is the level of such marker or parameter in a normal, otherwise unaffected cell population or tissue (e.g., a biological sample obtained from a healthy subject, or a level of the marker or parameter from a sample obtained from the subject at a prior time point, e.g., a biological sample obtained from a patient prior to being diagnosed with a disease or disorder, or a biological sample from an individual that has not been contacted with a therapeutic composition). It is contemplated that one can also use a biomarker or parameter from an individual whose cancer does respond to checkpoint inhibitor immunotherapy as a reference. Microsatellites as described herein are compared to those in reference human genome build GRCh37/hg19.

The term “statistically significant” or “significantly” refers to statistical significance and generally means a two standard deviation (2SD) or greater difference.

As used herein the term “comprising” or “comprises” is used in reference to compositions, methods, and respective component(s) thereof, that are essential to the method or composition, yet open to the inclusion of unspecified elements, whether essential or not.

The singular terms “a,” “an,” and “the” include plural referents unless context clearly indicates otherwise. Similarly, the word “or” is intended to include “and” unless the context clearly indicates otherwise. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of this disclosure, suitable methods and materials are described below. The abbreviation, “e.g.” is derived from the Latin exempli gratia, and is used herein to indicate a non-limiting example. Thus, the abbreviation “e.g.” is synonymous with the term “for example.”

Groupings of alternative elements or embodiments of the invention disclosed herein are not to be construed as limitations. Each group member can be referred to and claimed individually or in any combination with other members of the group or other elements found herein. One or more members of a group can be included in, or deleted from, a group for reasons of convenience and/or patentability. When any such inclusion or deletion occurs, the specification is herein deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims.

Other terms are defined herein within the description of the various aspects of the invention.

All patents and other publications; including literature references, issued patents, published patent applications, and co-pending patent applications; cited throughout this application are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the technology described herein. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representation as to the contents of these documents is based on the information available to the applicants and does not constitute any admission as to the correctness of the dates or contents of these documents.

The description of embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. While specific embodiments of, and examples for, the disclosure are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the disclosure, as those skilled in the relevant art will recognize. For example, while method steps or functions are presented in a given order, alternative embodiments may perform functions in a different order, or functions may be performed substantially concurrently. The teachings of the disclosure provided herein can be applied to other procedures or methods as appropriate. The various embodiments described herein can be combined to provide further embodiments. Aspects of the disclosure can be modified, if necessary, to employ the compositions, functions and concepts of the above references and application to provide yet further embodiments of the disclosure. These and other changes can be made to the disclosure in light of the detailed description. All such modifications are intended to be included within the scope of the appended claims.

Specific elements of any of the foregoing embodiments can be combined or substituted for elements in other embodiments. Furthermore, while advantages associated with certain embodiments of the disclosure have been described in the context of these embodiments, other embodiments may also exhibit such advantages, and not all embodiments need necessarily exhibit such advantages to fall within the scope of the disclosure.

The technology described herein is further illustrated by the following examples which in no way should be construed as being further limiting.

Some embodiments of the technology described herein can be defined according to any of the following numbered paragraphs:

-   1. A method of predicting whether a subject's cancer will respond to     checkpoint inhibitor immunotherapy, the method comprising:     -   (a) receiving microsatellite instability data for a defined set         of microsatellite repeat marker sequences in cells of the         subject's cancer; and     -   (b) processing the microsatellite instability data to output a         categorical measure of microsatellite instability high (MSI-H)         or microsatellite stable (MSS);     -   wherein when the subject's cancer is determined to exhibit         MSI-H, it is predicted that the cancer will respond to         checkpoint inhibitor immunotherapy, and when the subject's         cancer is determined to exhibit MSS, it is predicted that the         cancer is less likely to respond to checkpoint inhibitor         immunotherapy. -   2. A method of predicting whether a subject's cancer will respond to     checkpoint inhibitor immunotherapy, the method comprising:     -   determining microsatellite instability status for a defined set         of microsatellite repeat marker sequences in cells of the         subject's cancer,     -   wherein determining the microsatellite instability status of the         subject's cancer comprises:         -   (i) assaying loci in the defined set of microsatellite             repeat marker sequences in cells of the subject's cancer for             mutation, thereby generating microsatellite instability             data; and         -   (ii) processing the microsatellite instability data to             output a categorical measure of microsatellite instability             high (MSI-H) status or microsatellite stable (MSS) status             for the subject's cancer;         -   wherein when the subject's cancer is determined to exhibit             MSI-H, it is predicted that the cancer will respond to             checkpoint inhibitor immunotherapy, and when the subject's             cancer is determined to exhibit MSS, it is predicted that             the cancer is less likely to respond to checkpoint inhibitor             immunotherapy. -   3. The method of paragraph 1 or paragraph 2, wherein processing the     microsatellite instability data to output a categorical measure of     microsatellite instability high (MSI-H) or microsatellite stable     (MSS) comprises applying a quantitative model relating the     predictive capability of the markers in the set or a subset thereof     to known MSI status. -   4. The method of paragraph 3, wherein the quantitative model is     selected from a continuous measure, regression or weighted scoring     of markers, a combinatorial or decision-tree model, and a machine     learning model. -   5. The method of paragraph 4, wherein the continuous measure     comprises the proportion of unmutated or stable loci to mutated or     unstable loci detected in the set. -   6. The method of paragraph 4, wherein the quantitative model     comprises a random-forest model or a deep neural network machine     learning model. -   7. The method of paragraph 3, wherein the quantitative model     evaluates or incorporates consideration of one or more test     characteristics selected from the group consisting of sensitivity,     accuracy, correlation, probability, specificity, false-positive     rate, false negative rate, positive predictive value, negative     predictive value and area under the receiver-operator characteristic     (AUROC). -   8. The method of paragraph 7, wherein thresholds for the one or more     test characteristics indicative of MSI-H or MSS are defined within     parameters of the known test characteristics for a given clinical     application. -   9. The method of paragraph 1 or paragraph 2, wherein:     -   when the cancer is colon adenocarcinoma (COAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 1;     -   when the cancer is esophageal carcinoma (ESCA), the set of         microsatellite repeat marker sequences comprises a plurality up         to 503 of the microsatellites set out in Table 2;     -   when the cancer is glioblastoma multiforme (GBM), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 3;     -   when the cancer is lung adenocarcinoma (LUAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 4;     -   when the cancer is lung squamous cell carcinoma (LUSC), the set         of microsatellite repeat marker sequences comprises a plurality         up to 500 of the microsatellites set out in Table 5;     -   when the cancer is rectum adenocarcinoma (READ), the set of         microsatellite repeat marker sequences comprises a plurality up         to 501 of the microsatellites set out in Table 6;     -   when the cancer is stomach adenocarcinoma (STAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 7;     -   when the cancer is brain lower grade glioma (LGG), the set of         microsatellite repeat marker sequences comprises a plurality up         to 266 of the microsatellites set out in Table 8;     -   when the cancer is prostate adenocarcinoma (PRAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 9;     -   when the cancer is cervical squamous cell carcinoma (CESC), the         set of microsatellite repeat marker sequences comprises a         plurality up to 500 of the microsatellites set out in Table 10;     -   when the cancer is lymphoid neoplasm diffuse large B-cell         lymphoma (DLBC), the set of microsatellite repeat marker         sequences comprises a plurality up to 212 of the microsatellites         set out in Table 11;     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         the set of microsatellite repeat marker sequences comprises a         plurality up to 500 of the microsatellites set out in Table 12;     -   when the cancer is kidney renal clear cell carcinoma (KIRC), the         set of microsatellite repeat marker sequences comprises a         plurality up to 508 of the microsatellites set out in Table 13;     -   when the cancer is breast invasive carcinoma (BRCA), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 14A; and     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or         stomach adenocarcinoma (STAD), the set of microsatellite repeat         marker sequences comprises a plurality up to 37 of the         microsatellites set out in Table 21. -   10. The method of paragraph 1 or paragraph 2, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     200 of the sequences set out in the respective Table for the     subject's cancer type. -   11. The method of paragraph 1 or paragraph 2, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     300 of the sequences set out in the respective Table for the     subject's cancer type. -   12. The method of paragraph 1 or paragraph 2, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     the first 100 of the sequences set out in the respective Table for     the subject's cancer type. -   13. The method of paragraph 1 or paragraph 2, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     the first 200 of the sequences set out in the respective Table for     the subject's cancer type. -   14. The method of paragraph 1 or paragraph 2, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     the first 300 of the sequences set out in the respective Table for     the subject's cancer type. -   15. The method of any one of paragraphs 1-14, wherein the checkpoint     inhibitor immunotherapy is an inhibitor of a checkpoint molecule     selected from the group consisting of: PD-1 or PD-L1, CTLA4,     Adenosine A2A receptor (A2AR), CD276, CD39, CD73, B7 family immune     checkpoint molecules, V-set domain-containing T-cell activation     inhibitor 1 (B7H4), B and T Lymphocyte Attenuator (BTLA),     Indoleamine 2,3-dioxygenase (IDO), Killer-cell Immunoglobulin-like     Receptor (KIR), Lymphocyte Activation Gene-3 (LAG3), nicotinamide     adenine dinucleotide phosphate NADPH oxidase isoform 2 (NOX2),     T-cell Immunoglobulin domain and Mucin domain 3 (TIM-3), T cell     immunoreceptor with Ig and ITIM domains (TIGIT), V-domain Ig     suppressor of T cell activation (VISTA), and Sialic acid-binding     immunoglobulin-type lectin 7 (SIGLEC7). -   16. The method of any one of paragraphs 1-15, wherein the checkpoint     inhibitor is selected from the group consisting of pembrolizumab     (Keytruda®), nivolumab (Opdivo®), cemiplimab (Libtayo®),     spartalizumab, camrelizumab, sintilimab, tislelizumab, toripalimab,     dostarlimab, INVMGA00012, AMP-224, AMP-514, atezolizumab     (Tecentriq®), avelumab (Bavencio®), survalumab (Imfinzi®), KN035,     CK-301, AUNP12, CA-170, BMS-986189, and ipilimumab (Yervoy®). -   17. The method of paragraph 1 or paragraph 2, wherein the processing     of MSI-H or MSS is determined by a threshold value for the set of     microsatellite marker sequences. -   18. The method of paragraph 17, wherein the threshold for the set of     microsatellite marker sequences is determined using the percentage     of mutated microsatellite markers in the set to calculate the area     under the receiver operating characteristic (AUROC). -   19. The method of paragraph 18, wherein the smallest number of     markers in the set necessary to reach a selected AUROC value is the     threshold. -   20. The method of paragraph 19, wherein the selected AUROC value is     a value between 0.6 and 0.99, inclusive. -   21. The method of paragraph 19, wherein the selected AUROC value is     0.9 or more. -   22. The method of any one of paragraphs 1-21, wherein the checkpoint     inhibitor immunotherapy is an inhibitor of PD-1 or PD-L1. -   23. The method of any one of paragraphs 1-22, wherein the checkpoint     inhibitor immunotherapy comprises a checkpoint inhibitor antibody. -   24. The method of paragraph 2, wherein assaying loci in the defined     set of microsatellite repeat marker sequences in cells of the     subject's cancer for mutation comprises polynucleotide sequencing,     measurement of total mutational burden, immunohistochemical     analysis, and/or polymerase chain reaction. -   25. The method of paragraph 24, wherein polynucleotide sequencing     comprises whole genome sequencing, whole exome sequencing, or     targeted gene capture sequencing. -   26. The method of paragraph 1 or paragraph 2, wherein microsatellite     mutations correspond to those identified in reference human genome     GRCh37/hg19 translated to a different build of the human reference     genome. -   27. A method of determining microsatellite instability (MSI) in a     subject's cancer, the method comprising     -   assaying mutation status for a set of microsatellite repeat         marker sequences in cells of the subject's cancer, wherein when         the set of microsatellites exhibits mutation at or above a         threshold number of microsatellites in the set, the subject's         cancer is determined to exhibit high microsatellite instability         (MSI-H), and when the set of microsatellites exhibits mutation         below the threshold number of microsatellites in the set, the         subject's cancer is determined to exhibit microsatellite         stability (MSS);     -   wherein the threshold for the set is determined using the         percentage of mutated microsatellite markers in the set to         calculate the area under the receiver operating characteristic         (AUROC), and wherein the smallest number of markers in the set         necessary to reach an AUROC value selected in the range of 0.6         to 0.99, inclusive, is the threshold;     -   and wherein:     -   when the cancer is colon adenocarcinoma (COAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 1;     -   when the cancer is esophageal carcinoma (ESCA), the set of         microsatellite repeat marker sequences comprises a plurality up         to 503 of the microsatellites set out in Table 2;     -   when the cancer is glioblastoma multiforme (GBM), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 3;     -   when the cancer is lung adenocarcinoma (LUAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 4;     -   when the cancer is lung squamous cell carcinoma (LUSC), the set         of microsatellite repeat marker sequences comprises a plurality         up to 500 of the microsatellites set out in Table 5;     -   when the cancer is rectum adenocarcinoma (READ), the set of         microsatellite repeat marker sequences comprises a plurality up         to 501 of the microsatellites set out in Table 6;     -   when the cancer is stomach adenocarcinoma (STAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 7;     -   when the cancer is brain lower grade glioma (LGG), the set of         microsatellite repeat marker sequences comprises a plurality up         to 266 of the microsatellites set out in Table 8;     -   when the cancer is prostate adenocarcinoma (PRAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 9;     -   when the cancer is cervical squamous cell carcinoma (CESC), the         set of microsatellite repeat marker sequences comprises a         plurality up to 500 of the microsatellites set out in Table 10;     -   when the cancer is lymphoid neoplasm diffuse large B-cell         lymphoma (DLBC), the set of microsatellite repeat marker         sequences comprises a plurality up to 212 of the microsatellites         set out in Table 11;     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         the set of microsatellite repeat marker sequences comprises a         plurality up to 500 of the microsatellites set out in Table 12;     -   when the cancer is kidney renal clear cell carcinoma (KIRC), the         set of microsatellite repeat marker sequences comprises a         plurality up to 508 of the microsatellites set out in Table 13;     -   when the cancer is breast invasive carcinoma (BRCA), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 14A; and     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or         stomach adenocarcinoma (STAD), the set of microsatellite repeat         marker sequences comprises a plurality up to 37 of the         microsatellites set out in Table 21. -   28. The method of paragraph 27, wherein the threshold is an AUROC     value of 0.9. -   29. The method of paragraph 27, wherein the set of microsatellite     repeat marker sequences comprises a plurality up to 200 of the     sequences set out in the respective Table for the subject's cancer     type. -   30. The method of paragraph 27, wherein the set of microsatellite     repeat marker sequences comprises a plurality up to 300 of the     sequences set out in the respective Table for the subject's cancer     type. -   31. The method of paragraph 27, wherein the set of microsatellite     repeat marker sequences comprises a plurality up to the first 100 of     the sequences set out in the respective Table for the subject's     cancer type. -   32. The method of paragraph 27, wherein the set of microsatellite     repeat marker sequences comprises a plurality up to the first 200 of     the sequences set out in the respective Table for the subject's     cancer type. -   33. The method of paragraph 27, wherein the set of microsatellite     repeat marker sequences comprises a plurality up to the first 300 of     the sequences set out in the respective Table for the subject's     cancer type. -   34. The method of any one of paragraphs 27-33, wherein if the cancer     is determined to be MSI-H, the subject is administered an effective     amount of a checkpoint inhibitor immunotherapy. -   35. The method of any one of paragraphs 27-33, wherein if the cancer     is determined to not be MSI-H, the subject is administered an     effective amount of a non-checkpoint inhibitor cancer therapeutic. -   36. The method of paragraph 34, wherein the checkpoint inhibitor     immunotherapy is an inhibitor of a checkpoint molecule selected from     the group consisting of: PD-1 or PD-L1, CTLA4, Adenosine A2A     receptor (A2AR), CD276, CD39, CD73, B7 family immune checkpoint     molecules, V-set domain-containing T-cell activation inhibitor 1     (B7H4), B and T Lymphocyte Attenuator (BTLA), Indoleamine     2,3-dioxygenase (IDO), Killer-cell Immunoglobulin-like Receptor     (KIR), Lymphocyte Activation Gene-3 (LAG3), nicotinamide adenine     dinucleotide phosphate NADPH oxidase isoform 2 (NOX2), T-cell     Immunoglobulin domain and Mucin domain 3 (TIM-3), T cell     immunoreceptor with Ig and ITIM domains (TIGIT), V-domain Ig     suppressor of T cell activation (VISTA), and Sialic acid-binding     immunoglobulin-type lectin 7 (SIGLEC7). -   37. The method of any one of paragraphs 27-36, wherein the     checkpoint inhibitor is selected from the group consisting of     pembrolizumab (Keytruda®), nivolumab (Opdivo®), cemiplimab     (Libtayo®), spartalizumab, camrelizumab, sintilimab, tislelizumab,     toripalimab, dostarlimab, INVMGA00012, AMP-224, AMP-514,     atezolizumab (Tecentriq®), avelumab (Bavencio®), survalumab     (Imfinzi®), KN035, CK-301, AUNP12, CA-170, BMS-986189, and     ipilimumab (Yervoy®). -   38. The method of any one of paragraphs 27-37, wherein the     checkpoint inhibitor immunotherapy is an inhibitor of PD-1 or PD-L1. -   39. The method of any one of paragraphs 27-38, wherein the     checkpoint inhibitor immunotherapy comprises a checkpoint inhibitor     antibody. -   40. The method of any one of paragraphs 27-39, wherein assaying     mutation status comprises polynucleotide sequencing, measurement of     tumor mutational burden, inference of mutational signatures,     immunohistochemical analysis, and/or polymerase chain reaction. -   41. The method of paragraph 40, wherein polynucleotide sequencing     comprises whole genome sequencing, whole exome sequencing, or     targeted gene capture sequencing. -   42. The method of any one of paragraphs 27-41, wherein     microsatellite mutations correspond to those identified in reference     human genome GRCh37/hg19 translated to a different build of the     human reference genome. -   43. A method of treating cancer in a subject in need thereof, the     method comprising determining microsatellite instability status for     cells of a subject's cancer by a method of any one of paragraphs     1-42, and, when the microsatellite instability status is determined     to be MSI-H, administering a checkpoint inhibitor, or, when the     microsatellite instability status is determined to be MSS,     administering a non-checkpoint inhibitor cancer therapeutic. -   44. The method of paragraph 43, wherein the checkpoint inhibitor is     an inhibitor of a checkpoint molecule selected from the group     consisting of: PD-1 or PD-L1, CTLA4, Adenosine A2A receptor (A2AR),     CD276, CD39, CD73, B7 family immune checkpoint molecules, V-set     domain-containing T-cell activation inhibitor 1 (B7H4), B and T     Lymphocyte Attenuator (BTLA), Indoleamine 2,3-dioxygenase (IDO),     Killer-cell Immunoglobulin-like Receptor (KIR), Lymphocyte     Activation Gene-3 (LAG3), nicotinamide adenine dinucleotide     phosphate NADPH oxidase isoform 2 (NOX2), T-cell Immunoglobulin     domain and Mucin domain 3 (TIM-3), T cell immunoreceptor with Ig and     ITIM domains (TIGIT), V-domain Ig suppressor of T cell activation     (VISTA), and Sialic acid-binding immunoglobulin-type lectin 7     (SIGLEC7). -   45. The method of paragraph 43, wherein the checkpoint inhibitor is     selected from the group consisting of pembrolizumab (Keytruda®),     nivolumab (Opdivo®), cemiplimab (Libtayo®), spartalizumab,     camrelizumab, sintilimab, tislelizumab, toripalimab, dostarlimab,     INVMGA00012, AMP-224, AMP-514, atezolizumab (Tecentriq®), avelumab     (Bavencio®), survalumab (Imfinzi®), KN035, CK-301, AUNP12, CA-170,     BMS-986189, and ipilimumab (Yervoy®). -   46. The method of paragraph 43, wherein the checkpoint inhibitor is     an inhibitor of PD-1 or PD-L1. -   47. The method of paragraph 43, wherein the checkpoint inhibitor     comprises a checkpoint inhibitor antibody. -   48. The method of paragraph 43, wherein the non-checkpoint inhibitor     cancer therapy comprises one or more of angiostatin K1-3,     DL-a-Difluoromethyl-ornithine, endostatin, fumagillin, genistein,     minocycline, staurosporine, and (±)-thalidomide; a DNA     intercalator/cross-linker, such as Bleomycin, Carboplatin,     Carmustine, Chlorambucil, Cyclophosphamide, cis-Diammineplatinum(II)     dichloride (Cisplatin), Melphalan, Mitoxantrone, and Oxaliplatin; a     DNA synthesis inhibitor, such as (±)-Amethopterin (Methotrexate),     3-Amino-1,2,4-benzotriazine 1,4-dioxide, Aminopterin, Cytosine     β-D-arabinofuranoside, 5-Fluoro-5′-deoxyuridine, 5-Fluorouracil,     Ganciclovir, Hydroxyurea, and Mitomycin C; a DNA-RNA transcription     regulator, such as Actinomycin D, Daunorubicin, Doxorubicin,     Homoharringtonine, and Idarubicin; an enzyme inhibitor, such as     S(+)-Camptothecin, Curcumin, (−)-Deguelin, 5,6-Dichlorobenzimidazole     1-β-D-ribofuranoside, Etoposide, Formestane, Fostriecin, Hispidin,     2-Imino-1-imidazoli-dineacetic acid (Cyclocreatine), Mevinolin,     Trichostatin A, Tyrphostin AG 34, and Tyrphostin AG 879; a gene     regulator, such as 5-Aza-2′-deoxycytidine, 5-Azacytidine,     Cholecalciferol (Vitamin D3), 4-Hydroxytamoxifen, Melatonin,     Mifepristone, Raloxifene, all trans-Retinal (Vitamin A aldehyde),     Retinoic acid, all trans (Vitamin A acid), 9-cis-Retinoic Acid,     13-cis-Retinoic acid, Retinol (Vitamin A), Tamoxifen, and     Troglitazone; a microtubule inhibitor, such as Colchicine,     Dolastatin 15, Nocodazole, Paclitaxel, Podophyllotoxin, Rhizoxin,     Vinblastine, Vincristine, Vindesine, and Vinorelbine (Navelbine); a     neoantigen; and an unclassified antitumor agent, such as     17-(Allylamino)-17-demethoxygeldanamycin, 4-Amino-1,8-naphthalimide,     Apigenin, Brefeldin A, Cimetidine, Dichloromethylene-diphosphonic     acid, Leuprolide (Leuprorelin), Luteinizing Hormone-Releasing     Hormone, Pifithrin-α, Rapamycin, Sex hormone-binding globulin,     Thapsigargin, and Urinary trypsin inhibitor fragment (Bikunin),     Vemurafenib (Zelboraf®) imatinib mesylate (Gleevec®), erlotinib     (Tarceva®), gefitinib (Iressa®), Vismodegib (Erivedge™),     90Y-ibritumomab tiuxetan, regorafenib (Stivarga®), sunitinib     (Sutent®), Denosumab (Xgeva®), sorafenib (Nexavar®), pazopanib     (Votrient®), axitinib (Inlyta®), dasatinib (Sprycel®), nilotinib     (Tasigna®), bosutinib (Bosulif®), ofatumumab (Arzerra®),     obinutuzumab (Gazyva™), ibrutinib (Imbruvica™) idelalisib     (Zydelig®), crizotinib (Xalkori®), erlotinib (Tarceva®), afatinib     dimaleate (Gilotrif®), ceritinib (LDK378/Zykadia), ibritumomab     tiuxetan (Zevalin®), brentuximab vedotin (Adcetris®), bortezomib     (Velcade®), siltuximab (Sylvant™), trametinib (Mekinist®),     dabrafenib (Tafinlar®), a targeted therapy such as toremifene     (Fareston®), fulvestrant (Faslodex®), anastrozole (Arimidex®),     exemestane (Aromasin®), letrozole (Ferrara®), ziv-aflibercept     (Zaltrap®), Alitretinoin (Panretin®), temsirolimus (Torisel®),     Tretinoin (Vesanoid®), denileukin diftitox (Ontak®), vorinostat     (Zolinza®), romidepsin (Istodax®), bexarotene (Targretin®),     pralatrexate (Folotyn®), lenaliomide (Revlimid®), belinostat     (Beleodaq™), lenaliomide (Revlimid®), pomalidomide (Pomalyst®),     Cabazitaxel (Jevtana®), enzalutamide (Xtandi®), abiraterone acetate     (Zytiga®), radium 223 chloride (Xofigo®), or everolimus (Afinitor®),     an epigenetic targeted drug such as HDAC inhibitors, azacitidine     (Vidaza®), decitabine (Dacogen®), vorinostat (Zolinza®), romidepsin     (Istodax®), ruxolitinib (Jakafi®), kinase inhibitors, DNA     methyltransferase inhibitors, histone demethylase inhibitors, or     histone methylation inhibitors, and any derivative thereof.

49. A method of treating cancer in a subject in need thereof, wherein the subject's cancer has been determined to have a microsatellite instability status of MSI-H as determined by the method of any one of paragraphs 1-42, the method comprising administering an effective amount of a checkpoint inhibitor to the subject.

-   50. The method of paragraph 49, wherein the checkpoint inhibitor is     an inhibitor of a checkpoint molecule selected from the group     consisting of: PD-1 or PD-L1, CTLA4, Adenosine A2A receptor (A2AR),     CD276, CD39, CD73, B7 family immune checkpoint molecules, V-set     domain-containing T-cell activation inhibitor 1 (B7H4), B and T     Lymphocyte Attenuator (BTLA), Indoleamine 2,3-dioxygenase (IDO),     Killer-cell Immunoglobulin-like Receptor (KIR), Lymphocyte     Activation Gene-3 (LAG3), nicotinamide adenine dinucleotide     phosphate NADPH oxidase isoform 2 (NOX2), T-cell Immunoglobulin     domain and Mucin domain 3 (TIM-3), T cell immunoreceptor with Ig and     ITIM domains (TIGIT), V-domain Ig suppressor of T cell activation     (VISTA), and Sialic acid-binding immunoglobulin-type lectin 7     (SIGLEC7). -   51. The method of paragraph 49, wherein the checkpoint inhibitor is     selected from the group consisting of pembrolizumab (Keytruda®),     nivolumab (Opdivo®), cemiplimab (Libtayo®), spartalizumab,     camrelizumab, sintilimab, tislelizumab, toripalimab, dostarlimab,     INVMGA00012, AMP-224, AMP-514, atezolizumab (Tecentriq®), avelumab     (Bavencio®), survalumab (Imfinzi®), KN035, CK-301, AUNP12, CA-170,     BMS-986189, and ipilimumab (Yervoy®). -   52. The method of paragraph 49, wherein the checkpoint inhibitor is     an inhibitor of PD-1 or PD-L1. -   53. The method of paragraph 49, wherein the checkpoint inhibitor     comprises a checkpoint inhibitor antibody. -   54. The method of paragraph 49, wherein the non-checkpoint inhibitor     cancer therapy comprises one or more of angiostatin K1-3,     DL-α-Difluoromethyl-ornithine, endostatin, fumagillin, genistein,     minocycline, staurosporine, and (±)-thalidomide; a DNA     intercalator/cross-linker, such as Bleomycin, Carboplatin,     Carmustine, Chlorambucil, Cyclophosphamide, cis-Diammineplatinum(II)     dichloride (Cisplatin), Melphalan, Mitoxantrone, and Oxaliplatin; a     DNA synthesis inhibitor, such as (±)-Amethopterin (Methotrexate),     3-Amino-1,2,4-benzotriazine 1,4-dioxide, Aminopterin, Cytosine     β-D-arabinofuranoside, 5-Fluoro-5′-deoxyuridine, 5-Fluorouracil,     Ganciclovir, Hydroxyurea, and Mitomycin C; a DNA-RNA transcription     regulator, such as Actinomycin D, Daunorubicin, Doxorubicin,     Homoharringtonine, and Idarubicin; an enzyme inhibitor, such as     S(+)-Camptothecin, Curcumin, (−)-Deguelin, 5,6-Dichlorobenzimidazole     1-β-D-ribofuranoside, Etoposide, Formestane, Fostriecin, Hispidin,     2-Imino-1-imidazoli-dineacetic acid (Cyclocreatine), Mevinolin,     Trichostatin A, Tyrphostin AG 34, and Tyrphostin AG 879; a gene     regulator, such as 5-Aza-2′-deoxycytidine, 5-Azacytidine,     Cholecalciferol (Vitamin D3), 4-Hydroxytamoxifen, Melatonin,     Mifepristone, Raloxifene, all trans-Retinal (Vitamin A aldehyde),     Retinoic acid, all trans (Vitamin A acid), 9-cis-Retinoic Acid,     13-cis-Retinoic acid, Retinol (Vitamin A), Tamoxifen, and     Troglitazone; a microtubule inhibitor, such as Colchicine,     Dolastatin 15, Nocodazole, Paclitaxel, Podophyllotoxin, Rhizoxin,     Vinblastine, Vincristine, Vindesine, and Vinorelbine (Navelbine); a     neoantigen; and an unclassified antitumor agent, such as     17-(Allylamino)-17-demethoxygeldanamycin, 4-Amino-1,8-naphthalimide,     Apigenin, Brefeldin A, Cimetidine, Dichloromethylene-diphosphonic     acid, Leuprolide (Leuprorelin), Luteinizing Hormone-Releasing     Hormone, Pifithrin-α, Rapamycin, Sex hormone-binding globulin,     Thapsigargin, and Urinary trypsin inhibitor fragment (Bikunin),     Vemurafenib (Zelboraf®) imatinib mesylate (Gleevec®), erlotinib     (Tarceva®), gefitinib (Iressa®), Vismodegib (Erivedge™),     90Y-ibritumomab tiuxetan, regorafenib (Stivarga®), sunitinib     (Sutent®), Denosumab (Xgeva®), sorafenib (Nexavar®), pazopanib     (Votrient®), axitinib (Inlyta®), dasatinib (Sprycel®), nilotinib     (Tasigna®), bosutinib (Bosulif®), ofatumumab (Arzerra®),     obinutuzumab (Gazyva™), ibrutinib (Imbruvica™) idelalisib     (Zydelig®), crizotinib (Xalkori®), erlotinib (Tarceva®), afatinib     dimaleate (Gilotrif®), ceritinib (LDK378/Zykadia), ibritumomab     tiuxetan (Zevalin®), brentuximab vedotin (Adcetris®), bortezomib     (Velcade®), siltuximab (Sylvant™), trametinib (Mekinist®),     dabrafenib (Tafinlar®), a targeted therapy such as toremifene     (Fareston®), fulvestrant (Faslodex®), anastrozole (Arimidex®),     exemestane (Aromasin®), letrozole (Ferrara®), ziv-aflibercept     (Zaltrap®), Alitretinoin (Panretin®), temsirolimus (Torisel®),     Tretinoin (Vesanoid®), denileukin diftitox (Ontak®), vorinostat     (Zolinza®), romidepsin (Istodax®), bexarotene (Targretin®),     pralatrexate (Folotyn®), lenaliomide (Revlimid®), belinostat     (Beleodaq™), lenaliomide (Revlimid®), pomalidomide (Pomalyst®),     Cabazitaxel (Jevtana®), enzalutamide (Xtandi®), abiraterone acetate     (Zytiga®), radium 223 chloride (Xofigo®), or everolimus (Afinitor®),     an epigenetic targeted drug such as HDAC inhibitors, azacitidine     (Vidaza®), decitabine (Dacogen®), vorinostat (Zolinza®), romidepsin     (Istodax®), ruxolitinib (Jakafi®), kinase inhibitors, DNA     methyltransferase inhibitors, histone demethylase inhibitors, or     histone methylation inhibitors, and any derivative thereof. -   55. A method of predicting whether a subject's cancer will respond     to checkpoint inhibitor immunotherapy, the method comprising:     -   assaying mutation status for a set of microsatellite repeat         marker sequences in cells of the subject's cancer, wherein when         mutations are present in at least a threshold number of markers         in the set, the set provides at least 95% sensitivity and at         least 95% specificity for predicting high microsatellite         instability (MSI-H) for the subject's tumor,     -   wherein:     -   when the cancer is colon adenocarcinoma (COAD), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 1 and the threshold         number is 50%;     -   when the cancer is esophageal carcinoma (ESCA), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 2 and the threshold         number is 50%;     -   when the cancer is glioblastoma multiforme (GBM), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 3 and the threshold         number is 50%;     -   when the cancer is lung adenocarcinoma (LUAD), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 4 and the threshold         number is 50%;     -   when the cancer is lung squamous cell carcinoma (LUSC), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 5 and the threshold         number is 50%;     -   when the cancer is rectum adenocarcinoma (READ), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 6 and the threshold         number is 50%;     -   when the cancer is stomach adenocarcinoma (STAD), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 7 and the threshold         number is 25%;     -   when the cancer is brain lower grade glioma (LGG), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 8 and the threshold         number is 12.5%;     -   when the cancer is prostate adenocarcinoma (PRAD), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 9 and the threshold         number is 16.7%;     -   when the cancer is cervical squamous cell carcinoma (CESC), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 10 and the threshold         number is 45.8%;     -   when the cancer is lymphoid neoplasm diffuse large B-cell         lymphoma (DLBC), the microsatellite repeat marker sequences         comprise a plurality of microsatellite repeat markers in Table         11 and the threshold number is 25%;     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         the microsatellite repeat marker sequences comprise a plurality         of microsatellite repeat markers in Table 12 and the threshold         number is 12.9%;     -   when the cancer is kidney renal clear cell carcinoma (KIRC), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 13 and the threshold         number is 7.5%;     -   when the cancer is breast invasive carcinoma (BRCA), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 14A and the threshold         number is 3.6%; and     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or         stomach adenocarcinoma (STAD), the microsatellite repeat marker         sequences comprise a plurality of microsatellite repeat markers         in Table 21 and the threshold number is at least 12.9% (e.g.,         12.9%, 25%, 50%);     -   and wherein     -   when the subject's cancer exhibits greater than or equal to the         threshold number of mutations for that tumor type in the set,         the subject's cancer is determined to be MSI-H, and is predicted         to be sensitive to checkpoint inhibitor immunotherapy. -   56. The method of paragraph 55, wherein the checkpoint inhibitor     immunotherapy is an inhibitor of a checkpoint molecule selected from     the group consisting of: PD-1 or PD-L1, CTLA4, Adenosine A2A     receptor (A2AR), CD276, CD39, CD73, B7 family immune checkpoint     molecules, V-set domain-containing T-cell activation inhibitor 1     (B7H4), B and T Lymphocyte Attenuator (BTLA), Indoleamine     2,3-dioxygenase (IDO), Killer-cell Immunoglobulin-like Receptor     (KIR), Lymphocyte Activation Gene-3 (LAG3), nicotinamide adenine     dinucleotide phosphate NADPH oxidase isoform 2 (NOX2), T-cell     Immunoglobulin domain and Mucin domain 3 (TIM-3), T cell     immunoreceptor with Ig and ITIM domains (TIGIT), V-domain Ig     suppressor of T cell activation (VISTA), and Sialic acid-binding     immunoglobulin-type lectin 7 (SIGLEC7). -   57. The method of paragraph 55 or 56, wherein the checkpoint     inhibitor is selected from the group consisting of pembrolizumab     (Keytruda®), nivolumab (Opdivo®), cemiplimab (Libtayo®),     spartalizumab, camrelizumab, sintilimab, tislelizumab, toripalimab,     dostarlimab, INVMGA00012, AMP-224, AMP-514, atezolizumab     (Tecentriq®), avelumab (Bavencio®), survalumab (Imfinzi®), KN035,     CK-301, AUNP12, CA-170, BMS-986189, and ipilimumab (Yervoy®). -   58. The method of any one of paragraphs 55-57, wherein the     checkpoint inhibitor immunotherapy is an inhibitor of PD-1 or PD-L1. -   59. The method of any one of paragraphs 55-58, wherein the     checkpoint inhibitor immunotherapy comprises a checkpoint inhibitor     antibody. -   60. The method of any one of paragraphs 55-59, wherein assaying     mutation status comprises polynucleotide sequencing, measurement of     tumor mutational burden, inference of mutational signatures,     immunohistochemical analysis, and/or polymerase chain reaction. -   61. The method of paragraph 60, wherein polynucleotide sequencing     comprises whole genome sequencing, whole exome sequencing, or     targeted gene capture sequencing. -   62. The method of any one of paragraphs 55-61, wherein     microsatellite mutations correspond to those identified in reference     human genome GRCh37/hg19 translated to a different build of the     human reference genome. -   63. The method of any one of paragraphs 55-62, wherein if the     subject is predicted to be sensitive to the checkpoint inhibitor     immunotherapy, the subject is administered an effective amount of     the checkpoint inhibitor immunotherapy. -   64. The method of any one of paragraphs 55-62, wherein if the     subject is predicted to not be sensitive to the checkpoint inhibitor     immunotherapy, the subject is administered an effective amount of a     non-checkpoint inhibitor cancer therapeutic. -   65. A method of determining microsatellite instability (MSI) in a     subject's cancer, the method comprising:     -   assaying mutation status for a set of microsatellite repeat         marker sequences in the cells of the subject's cancer, wherein         when mutations are present in at least a threshold number of         markers in the set, the set provides at least 95% sensitivity         and at least 95% specificity for predicting high microsatellite         instability (MSI-H) for the subject's tumor,     -   wherein:     -   when the cancer is colon adenocarcinoma (COAD), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 1 and the threshold         number is 50%;     -   when the cancer is esophageal carcinoma (ESCA), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 2 and the threshold         number is 50%;     -   when the cancer is glioblastoma multiforme (GBM), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 3 and the threshold         number is 50%;     -   when the cancer is lung adenocarcinoma (LUAD), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 4 and the threshold         number is 50%;     -   when the cancer is lung squamous cell carcinoma (LUSC), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 5 and the threshold         number is 50%;     -   when the cancer is rectum adenocarcinoma (READ), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 6 and the threshold         number is 50%;     -   when the cancer is stomach adenocarcinoma (STAD), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 7 and the threshold         number is 25%;     -   when the cancer is brain lower grade glioma (LGG), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 8 and the threshold         number is 12.5%;     -   when the cancer is prostate adenocarcinoma (PRAD), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 9 and the threshold         number is 16.7%;     -   when the cancer is cervical squamous cell carcinoma (CESC), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 10 and the threshold         number is 45.8%;     -   when the cancer is lymphoid neoplasm diffuse large B-cell         lymphoma (DLBC), the microsatellite repeat marker sequences         comprise a plurality of microsatellite repeat markers in Table         11 and the threshold number is 25%;     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         the microsatellite repeat marker sequences comprise a plurality         of microsatellite repeat markers in Table 12 and the threshold         number is 12.9%;     -   when the cancer is kidney renal clear cell carcinoma (KIRC), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 13 and the threshold         number is 7.5%;     -   when the cancer is breast invasive carcinoma (BRCA), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 14A and the threshold         number is 3.6%; and     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or         stomach adenocarcinoma (STAD), the microsatellite repeat marker         sequences comprise a plurality of microsatellite repeat markers         in Table 21 and the threshold number is at least 12.9% (e.g.,         12.9%, 25%, 50%); and     -   wherein, cancer that exhibits greater than or equal to the         threshold number of mutations for that tumor type in the set is         determined to be MSI-H, and     -   cancer that exhibits fewer than the threshold number of         mutations for that tumor type in the set, the subject's cancer         is determined to be microsatellite stable or not MSI-H. -   66. The method of paragraph 65, wherein assaying mutation status     comprises polynucleotide sequencing, measurement of tumor mutational     burden, inference of mutational signatures, immunohistochemical     analysis, and/or polymerase chain reaction. -   67. The method of paragraph 66, wherein polynucleotide sequencing     comprises whole genome sequencing, whole exome sequencing, or     targeted gene capture sequencing. -   68. The method of any one of paragraphs 65-67, wherein     microsatellite mutations correspond to those identified in reference     human genome GRCh37/hg19 translated to a different build of the     human reference genome. -   69. The method of any one of paragraphs 65-68, wherein if the cancer     is determined to be MSI-H, the subject is administered an effective     amount of a checkpoint inhibitor immunotherapy. -   70. The method of any one of paragraphs 65-68, wherein if the cancer     is determined to not be MSI-H, the subject is administered an     effective amount of a non-checkpoint inhibitor cancer therapeutic. -   71. A method of treating cancer in a subject in need thereof, the     method comprising:     -   assaying mutation status for a set of microsatellite repeat         marker sequences in cells of the subject's cancer, wherein when         mutations are present in at least a threshold number of markers         in the set, and the set provides at least 95% sensitivity and at         least 95% specificity for predicting high microsatellite         instability (MSI-H) for the subject's tumor,     -   wherein:     -   when the cancer is colon adenocarcinoma (COAD), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 1 and the threshold         number is 50%;     -   when the cancer is esophageal carcinoma (ESCA), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 2 and the threshold         number is 50%;     -   when the cancer is glioblastoma multiforme (GBM), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 3 and the threshold         number is 50%;     -   when the cancer is lung adenocarcinoma (LUAD), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 4 and the threshold         number is 50%;     -   when the cancer is lung squamous cell carcinoma (LUSC), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 5 and the threshold         number is 50%;     -   when the cancer is rectum adenocarcinoma (READ), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 6 and the threshold         number is 50%;     -   when the cancer is stomach adenocarcinoma (STAD), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 7 and the threshold         number is 25%;     -   when the cancer is brain lower grade glioma (LGG), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 8 and the threshold         number is 12.5%;     -   when the cancer is prostate adenocarcinoma (PRAD), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 9 and the threshold         number is 16.7%;     -   when the cancer is cervical squamous cell carcinoma (CESC), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 10 and the threshold         number is 45.8%;     -   when the cancer is lymphoid neoplasm diffuse large B-cell         lymphoma (DLBC), the microsatellite repeat marker sequences         comprise a plurality of microsatellite repeat markers in Table         11 and the threshold number is 25%;     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         the microsatellite repeat marker sequences comprise a plurality         of microsatellite repeat markers in Table 12 and the threshold         number is 12.9%;     -   when the cancer is kidney renal clear cell carcinoma (KIRC), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 13 and the threshold         number is 7.5%;     -   when the cancer is breast invasive carcinoma (BRCA), the         microsatellite repeat marker sequences comprise a plurality of         microsatellite repeat markers in Table 14A and the threshold         number is 3.6%; and     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or         stomach adenocarcinoma (STAD), the microsatellite repeat marker         sequences comprise a plurality of microsatellite repeat markers         in Table 21 and the threshold number is at least 12.9% (e.g.,         12.9%, 25%, 50%); and     -   wherein     -   when the subject's cancer exhibits greater than or equal to the         threshold number of mutations for that tumor type in the set,         administering a checkpoint inhibitor immunotherapy, and     -   when the subject's cancer exhibits fewer than the threshold         number of mutations for that tumor type in the set,         administering a non-checkpoint inhibitor cancer therapy. -   72. The method of paragraph 71, wherein assaying mutation status     comprises polynucleotide sequencing, measurement of tumor mutational     burden, inference of mutational signatures, immunohistochemical     analysis, and/or polymerase chain reaction. -   73. The method of paragraph 72, wherein polynucleotide sequencing     comprises whole genome sequencing, whole exome sequencing, or     targeted gene capture sequencing. -   74. The method of any one of paragraphs 71-73, wherein     microsatellite mutations correspond to those identified in reference     human genome GRCh37/hg19 translated to a different build of the     human reference genome. -   75. Use of a checkpoint inhibitor in a method for the treatment of     cancer, the method comprising:     -   (a) receiving microsatellite instability data for a defined set         of microsatellite repeat marker sequences in cells of the         subject's cancer; and     -   (b) processing the microsatellite instability data to output a         categorical measure of microsatellite instability high (MSI-H)         or microsatellite stable (MSS);     -   wherein the checkpoint inhibitor is administered when the         subject's cancer is determined to exhibit MSI-H. -   76. Use of a checkpoint inhibitor in a method for the treatment of     cancer, the method comprising:     -   determining microsatellite instability status for a defined set         of microsatellite repeat marker sequences in cells of the         subject's cancer,     -   wherein determining the microsatellite instability status of the         subject's cancer comprises:         -   (i) assaying loci in the defined set of microsatellite             repeat marker sequences in cells of the subject's cancer for             mutation, thereby generating microsatellite instability             data; and         -   (ii) processing the microsatellite instability data to             output a categorical measure of microsatellite instability             high (MSI-H) status or microsatellite stable (MSS) status             for the subject's cancer;         -   wherein the checkpoint inhibitor is administered when the             subject's cancer is determined to exhibit MSI-H. -   77. The use of paragraph 75 or paragraph 76, wherein processing the     microsatellite instability data to output a categorical measure of     microsatellite instability high (MSI-H) or microsatellite stable     (MSS) comprises applying a quantitative model relating the     predictive capability of the markers in the set or a subset thereof     to known MSI status. -   78. The use of paragraph 77, wherein the quantitative model is     selected from a continuous measure, regression or weighted scoring     of markers, a combinatorial or decision-tree model, and a machine     learning model. -   79. The use of paragraph 78, wherein the continuous measure     comprises the proportion of unmutated or stable loci to mutated or     unstable loci detected in the set. -   80. The use of paragraph 78, wherein the quantitative model     comprises a random-forest model or a deep neural network machine     learning model. -   81. The use of paragraph 77, wherein the quantitative model     evaluates or incorporates consideration of one or more test     characteristics selected from the group consisting of sensitivity,     accuracy, correlation, probability, specificity, false-positive     rate, false negative rate, positive predictive value, negative     predictive value and area under the receiver-operator characteristic     (AUROC). -   82. The use of paragraph 81, wherein thresholds for the one or more     test characteristics indicative of MSI-H or MSS are defined within     parameters of the known test characteristics for a given clinical     application. -   83. The use of paragraph 75 or paragraph 76, wherein:     -   when the cancer is colon adenocarcinoma (COAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 1;     -   when the cancer is esophageal carcinoma (ESCA), the set of         microsatellite repeat marker sequences comprises a plurality up         to 503 of the microsatellites set out in Table 2;     -   when the cancer is glioblastoma multiforme (GBM), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 3;     -   when the cancer is lung adenocarcinoma (LUAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 4;     -   when the cancer is lung squamous cell carcinoma (LUSC), the set         of microsatellite repeat marker sequences comprises a plurality         up to 500 of the microsatellites set out in Table 5;     -   when the cancer is rectum adenocarcinoma (READ), the set of         microsatellite repeat marker sequences comprises a plurality up         to 501 of the microsatellites set out in Table 6;     -   when the cancer is stomach adenocarcinoma (STAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 7;     -   when the cancer is brain lower grade glioma (LGG), the set of         microsatellite repeat marker sequences comprises a plurality up         to 266 of the microsatellites set out in Table 8;     -   when the cancer is prostate adenocarcinoma (PRAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 9;     -   when the cancer is cervical squamous cell carcinoma (CESC), the         set of microsatellite repeat marker sequences comprises a         plurality up to 500 of the microsatellites set out in Table 10;     -   when the cancer is lymphoid neoplasm diffuse large B-cell         lymphoma (DLBC), the set of microsatellite repeat marker         sequences comprises a plurality up to 212 of the microsatellites         set out in Table 11;     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         the set of microsatellite repeat marker sequences comprises a         plurality up to 500 of the microsatellites set out in Table 12;     -   when the cancer is kidney renal clear cell carcinoma (KIRC), the         set of microsatellite repeat marker sequences comprises a         plurality up to 508 of the microsatellites set out in Table 13;     -   when the cancer is breast invasive carcinoma (BRCA), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 14A; and     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or         stomach adenocarcinoma (STAD), the set of microsatellite repeat         marker sequences comprises a plurality up to 37 of the         microsatellites set out in Table 21. -   84. The use of paragraph 75 or paragraph 76, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     200 of the sequences set out in the respective Table for the     subject's cancer type. -   85. The use of paragraph 75 or paragraph 76, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     300 of the sequences set out in the respective Table for the     subject's cancer type. -   86. The use of paragraph 75 or paragraph 76, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     the first 100 of the sequences set out in the respective Table for     the subject's cancer type. -   87. The use of paragraph 75 or paragraph 76, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     the first 200 of the sequences set out in the respective Table for     the subject's cancer type. -   88. The use of paragraph 75 or paragraph 76, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     the first 300 of the sequences set out in the respective Table for     the subject's cancer type. -   89. The use of any one of paragraphs 75-88, wherein the checkpoint     inhibitor immunotherapy is an inhibitor of a checkpoint molecule     selected from the group consisting of: PD-1 or PD-L1, CTLA4,     Adenosine A2A receptor (A2AR), CD276, CD39, CD73, B7 family immune     checkpoint molecules, V-set domain-containing T-cell activation     inhibitor 1 (B7H4), B and T Lymphocyte Attenuator (BTLA),     Indoleamine 2,3-dioxygenase (IDO), Killer-cell Immunoglobulin-like     Receptor (KIR), Lymphocyte Activation Gene-3 (LAG3), nicotinamide     adenine dinucleotide phosphate NADPH oxidase isoform 2 (NOX2),     T-cell Immunoglobulin domain and Mucin domain 3 (TIM-3), T cell     immunoreceptor with Ig and ITIM domains (TIGIT), V-domain Ig     suppressor of T cell activation (VISTA), and Sialic acid-binding     immunoglobulin-type lectin 7 (SIGLEC7). -   90. The use of any one of paragraphs 75-89, wherein the checkpoint     inhibitor is selected from the group consisting of pembrolizumab     (Keytruda®), nivolumab (Opdivo®), cemiplimab (Libtayo®),     spartalizumab, camrelizumab, sintilimab, tislelizumab, toripalimab,     dostarlimab, INVMGA00012, AMP-224, AMP-514, atezolizumab     (Tecentriq®), avelumab (Bavencio®), survalumab (Imfinzi®), KN035,     CK-301, AUNP12, CA-170, BMS-986189, and ipilimumab (Yervoy®). -   91. The use of paragraph 75 or paragraph 76, wherein the processing     of MSI-H or MSS is determined by a threshold value for the set of     microsatellite marker sequences. -   92. The use of paragraph 91, wherein the threshold for the set of     microsatellite marker sequences is determined using the percentage     of mutated microsatellite markers in the set to calculate the area     under the receiver operating characteristic (AUROC). -   93. The use of paragraph 92, wherein the smallest number of markers     in the set necessary to reach a selected AUROC value is the     threshold. -   94. The use of paragraph 93, wherein the selected AUROC value is a     value between 0.6 and 0.99, inclusive. -   95. The use of paragraph 93, wherein the selected AUROC value is 0.9     or more. -   96. The use of any one of paragraphs 75-95, wherein the checkpoint     inhibitor immunotherapy is an inhibitor of PD-1 or PD-L1. -   97. The use of any one of paragraphs 75-96, wherein the checkpoint     inhibitor immunotherapy comprises a checkpoint inhibitor antibody. -   98. The use of paragraph 76, wherein assaying loci in the defined     set of microsatellite repeat marker sequences in cells of the     subject's cancer for mutation comprises polynucleotide sequencing,     measurement of total mutational burden, immunohistochemical     analysis, and/or polymerase chain reaction. -   99. The use of paragraph 98, wherein polynucleotide sequencing     comprises whole genome sequencing, whole exome sequencing, or     targeted gene capture sequencing. -   100. The use of paragraph 75 or paragraph 76, wherein microsatellite     mutations correspond to those identified in reference human genome     GRCh37/hg19 translated to a different build of the human reference     genome. -   101. A diagnostic kit for determining microsatellite instability in     a cancer, the kit comprising reagents that permit the detection of     microsatellite mutation in a set of microsatellite repeat marker     sequences in the cancer, wherein:     -   when the cancer is colon adenocarcinoma (COAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 1;     -   when the cancer is esophageal carcinoma (ESCA), the set of         microsatellite repeat marker sequences comprises a plurality up         to 503 of the microsatellites set out in Table 2;     -   when the cancer is glioblastoma multiforme (GBM), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 3;     -   when the cancer is lung adenocarcinoma (LUAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 4;     -   when the cancer is lung squamous cell carcinoma (LUSC), the set         of microsatellite repeat marker sequences comprises a plurality         up to 500 of the microsatellites set out in Table 5;     -   when the cancer is rectum adenocarcinoma (READ), the set of         microsatellite repeat marker sequences comprises a plurality up         to 501 of the microsatellites set out in Table 6;     -   when the cancer is stomach adenocarcinoma (STAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 7;     -   when the cancer is brain lower grade glioma (LGG), the set of         microsatellite repeat marker sequences comprises a plurality up         to 266 of the microsatellites set out in Table 8;     -   when the cancer is prostate adenocarcinoma (PRAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 9;     -   when the cancer is cervical squamous cell carcinoma (CESC), the         set of microsatellite repeat marker sequences comprises a         plurality up to 500 of the microsatellites set out in Table 10;     -   when the cancer is lymphoid neoplasm diffuse large B-cell         lymphoma (DLBC), the set of microsatellite repeat marker         sequences comprises a plurality up to 212 of the microsatellites         set out in Table 11;     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         the set of microsatellite repeat marker sequences comprises a         plurality up to 500 of the microsatellites set out in Table 12;     -   when the cancer is kidney renal clear cell carcinoma (KIRC), the         set of microsatellite repeat marker sequences comprises a         plurality up to 508 of the microsatellites set out in Table 13;     -   when the cancer is breast invasive carcinoma (BRCA), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 14A; and     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or         stomach adenocarcinoma (STAD), the set of microsatellite repeat         marker sequences comprises a plurality up to 37 of the         microsatellites set out in Table 21. -   102. The diagnostic kit for determining microsatellite instability     of paragraph 101, wherein the set of microsatellite repeat marker     sequences comprises a plurality up to 200 of the sequences set out     in the respective Table for the subject's cancer type. -   103. The diagnostic kit for determining microsatellite instability     of paragraph 101, wherein the set of microsatellite repeat marker     sequences comprises a plurality up to 300 of the sequences set out     in the respective Table for the subject's cancer type. -   104. The diagnostic kit for determining microsatellite instability     of paragraph 101, wherein the set of microsatellite repeat marker     sequences comprises a plurality up to the first 100 of the sequences     set out in the respective Table for the subject's cancer type. -   105. The diagnostic kit for determining microsatellite instability     of paragraph 101, wherein the set of microsatellite repeat marker     sequences comprises a plurality up to the first 200 of the sequences     set out in the respective Table for the subject's cancer type. -   106. The diagnostic kit for determining microsatellite instability     of paragraph 101, wherein the set of microsatellite repeat marker     sequences comprises a plurality up to the first 300 of the sequences     set out in the respective Table for the subject's cancer type. -   107. The diagnostic kit of any one of paragraphs 101-106, wherein     the reagents comprise PCR primers that permit amplification of     members of the set of microsatellite repeat marker sequences. -   108. The diagnostic kit of paragraph 107, wherein the kit comprises     an array of reagents that permit the detection of microsatellite     mutation on a solid support. -   109. An array for detecting microsatellite instability in a cancer,     the array comprising nucleic acids that permit the detection of     microsatellite mutation in a set of microsatellite repeat marker     sequences in the cancer, wherein the nucleic acids are linked to a     solid support. -   110. The array of paragraph 109, wherein the nucleic acids are     complementary to at least a portion of the microsatellite sequences. -   111. The array of paragraph 109 or paragraph 110 wherein:     -   when the cancer is colon adenocarcinoma (COAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 1;     -   when the cancer is esophageal carcinoma (ESCA), the set of         microsatellite repeat marker sequences comprises a plurality up         to 503 of the microsatellites set out in Table 2;     -   when the cancer is glioblastoma multiforme (GBM), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 3;     -   when the cancer is lung adenocarcinoma (LUAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 4;     -   when the cancer is lung squamous cell carcinoma (LUSC), the set         of microsatellite repeat marker sequences comprises a plurality         up to 500 of the microsatellites set out in Table 5;     -   when the cancer is rectum adenocarcinoma (READ), the set of         microsatellite repeat marker sequences comprises a plurality up         to 501 of the microsatellites set out in Table 6;     -   when the cancer is stomach adenocarcinoma (STAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 7;     -   when the cancer is brain lower grade glioma (LGG), the set of         microsatellite repeat marker sequences comprises a plurality up         to 266 of the microsatellites set out in Table 8;     -   when the cancer is prostate adenocarcinoma (PRAD), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 9;     -   when the cancer is cervical squamous cell carcinoma (CESC), the         set of microsatellite repeat marker sequences comprises a         plurality up to 500 of the microsatellites set out in Table 10;     -   when the cancer is lymphoid neoplasm diffuse large B-cell         lymphoma (DLBC), the set of microsatellite repeat marker         sequences comprises a plurality up to 212 of the microsatellites         set out in Table 11;     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         the set of microsatellite repeat marker sequences comprises a         plurality up to 500 of the microsatellites set out in Table 12;     -   when the cancer is kidney renal clear cell carcinoma (KIRC), the         set of microsatellite repeat marker sequences comprises a         plurality up to 508 of the microsatellites set out in Table 13;     -   when the cancer is breast invasive carcinoma (BRCA), the set of         microsatellite repeat marker sequences comprises a plurality up         to 500 of the microsatellites set out in Table 14A; and     -   when the cancer is uterine corpus endometrial carcinoma (UCEC),         colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or         stomach adenocarcinoma (STAD), the set of microsatellite repeat         marker sequences comprises a plurality up to 37 of the         microsatellites set out in Table 21. -   112. The array of any one of paragraphs 109-111, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     200 of the sequences set out in the respective Table for the     subject's cancer type. -   113. The array of any one of paragraphs 109-111, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     300 of the sequences set out in the respective Table for the     subject's cancer type. -   114. The array of any one of paragraphs 109-111, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     the first 100 of the sequences set out in the respective Table for     the subject's cancer type. -   115. The array of any one of paragraphs 109-111, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     the first 200 of the sequences set out in the respective Table for     the subject's cancer type. -   116. The array of any one of paragraphs 109-111, wherein the set of     microsatellite repeat marker sequences comprises a plurality up to     the first 300 of the sequences set out in the respective Table for     the subject's cancer type. -   117. The array of any one of paragraphs 109-111, wherein the nucleic     acids comprise PCR primers that permit amplification of members of     the set of microsatellite repeat marker sequences.

EXAMPLES Example 1: Optimal Diagnostic Markers for MSI

Microsatellite instability (MSI) predicts oncological response to checkpoint blockade immunotherapies. Although microsatellite mutation is pathognomonic for the condition, loci have unequal diagnostic value for predicting MSI within and across cancer types.

METHODS SUMMARY: To better inform molecular diagnosis of MSI, 9,438 tumor-normal exome pairs and 901 whole genome sequence pairs from 33 different cancer types were examined, and genome-wide microsatellite instability events were cataloged. Using a statistical framework, microsatellite mutations were identified that were predictive of MSI within and across cancer types. The diagnostic accuracy of different subsets of maximally informative markers was estimated computationally using a dedicated validation set.

RESULTS SUMMARY: Twenty-five cancer types exhibited hypermutated states consistent with MSI. Recurrently mutated microsatellites associated with MSI were identifiable in 15 cancer types, but were largely specific to individual cancer types. Cancer-specific microsatellite panels of one to seven loci were needed to attain 95% diagnostic sensitivity and specificity for 11 cancer types, and in eight of the cancer types, 100% sensitivity and specificity were achieved. Breast cancer required 800 loci to achieve comparable performance, and recurrent microsatellite mutations were not identified supporting reliable MSI diagnosis in ovarian tumors. Features associated with informative microsatellites were cataloged.

CONCLUSION SUMMARY: Most microsatellites informative for MSI are specific to particular cancer types, requiring the use of tissue-specific loci for optimal diagnosis. Limited numbers of markers are needed to provide accurate MSI diagnosis in most tumor types, but it is challenging to diagnose breast and ovarian cancers using pre-defined microsatellite locus panels.

Background

Microsatellite instability (MSI) is a molecular tumor phenotype that is indicative of genomic hypermutability, usually reflecting inactivation of the mismatch repair (MMR) system. MSI is marked by spontaneous gains or losses of nucleotides from repetitive DNA tracts, resulting in new alleles of differing length that serve as the basis for its clinical diagnosis. Although classically associated with colorectal and endometrial tumors, MSI has now been recognized in most cancer types with varying prevalence and is accompanied by a generally increased rate of mutations genome-wide. Testing for MSI has subsequently emerged as a pan-cancer biomarker of therapeutic response to PDL-1 and PD-1 immune checkpoint inhibitors, where the MSI positive (microsatellite high, or MSI-H) phenotype is believed to serve as an indicator of mutation-associated neoantigens that permit a more robust T lymphocyte response than for MSI negative (microsatellite stable, or MSS) cases.

Molecular diagnosis of MSI in clinical practice is most commonly achieved using multiplexed PCR of defined microsatellite loci, followed by capillary electrophoresis to qualitatively detect new alleles (MSI-PCR). Quantitative next-generation sequencing (NGS) methods have been developed to identify MSI by assessing overall microsatellite mutation frequency at repetitive loci that are either directly targeted or incidentally captured by targeted gene enrichment oncology panels. Nevertheless, both conventional and NGS approaches interrogate markedly limited subsets of the millions of microsatellite markers available in the human genome: only five loci are included in standard MSI-PCR, whereas dozens to hundreds of sites are examined by typical NGS approaches.

Studies have revealed tissue-specific signatures of microsatellite mutation, such that alterations in specific loci can occur with disparate frequencies in tumors from different tissues. Consequently, microsatellites that are diagnostic for MSI potentially have unequal prognostic value within and across tumor types, such that loci useful in one cancer type may not yield accurate diagnoses in others. Supporting this hypothesis, standard MSI-PCR markers were developed for use in colon cancers and can exhibit poor performance in other malignancies.

The choice of markers is therefore critical to maximize sensitivity and specificity of molecular MSI diagnosis, regardless of whether testing is performed by conventional or NGS methods. Nevertheless, little effort to date has focused on using systematic, genome-scale analysis to identify optimal microsatellite loci for diagnosing MSI. Here, tumor-normal pairs of exome and whole genome data from 33 different cancer types were systematically evaluated in order to ascertain the most informative microsatellites for predicting MSI.

Methods: Sequence Data and Identification of Microsatellite Loci

Genomic microsatellite loci were identified as previously, with some modifications; see e.g., Hause et al. Nat Med. 2016, 22:1342-50, the contents of which are incorporated herein by reference in its entirety. Briefly, microsatellites were defined in the human genome (GRCh37/hg19; see e.g., Table 18 for sequence references) as repeating subunits of 1-5 bp in length and comprising ≥5 repeats using MISA. Adjacent microsatellites within ten base pairs of each other were termed ‘complex’ (c*) single loci if comprised of tracts with different repeating subunit lengths or ‘compound’ (c) single loci for those having the same repeat length. This analysis defined 19,035,602 loci, of which the 18,882,838 present on autosomes and chromosome X were retained. Repeat features were annotated using ANNOVAR (24 Feb. 2014 release).

Sequence alignments of tumors and patient-matched normal specimens from exome and whole genome sequencing projects were obtained from TCGA Research Network (see e.g., cancergenome.nih.gov/). Alignments were standardized prior to analysis by converting alignments to FASTQ files using PICARD v1.98, re-aligning to GRCh37/hg19 using BWA-MEM v0.7.12, and indexing with SamTools v1.1.

Cataloging Microsatellite Instability Events.

For each tumor and normal specimen, the number of sequence reads supporting different tract lengths at each locus were quantified using mSINGS (Git Commit ID a7e9ea9).

To identify instability events, multinomial distributions of allele lengths for tumor at each locus were compared to the joint multinomial distribution of allele lengths across tumor and normal at the site by:

(X _(wildtype_allele) ,X _(alternative_allele_1) , . . . X _(alternative_allele_i))˜Mult(n,p)

where which n refers to the number of reads at a site and p refers to the proportion supporting each alternative allelic length. “Unstable” microsatellites (those evidencing somatic mutations) were defined as those with nominally significant differences (p<0.05) by likelihood ratio (G) tests without continuity correction. Rates for calling false positive instability at this heuristic threshold were estimated as <3% at all sites having ≥2 reads in tumor and ≥1 read in its paired normal by simulating and comparing two distributions of 1,000 normal sites with median observed multinomial distributions of allele lengths by:

Mult(n=read_depth,P=0.9_(wildtype_allele),0.1_(alternative_alleles))

To confidently define “stable” sites in tumor (those lacking somatic mutations), sites were simulated from empirically observed multinomial read distributions for highly unstable sites in cases having >30 read coverage in both tumor and normal by:

Mult(1000,p=0.4_(wildtype_allele),0.6_(alternative_alleles))

Down-sampling analyses estimated that ≥18 reads per site yielded 95% power for identifying an unstable locus, providing strong evidence to conclude that a site was “stable” if no difference in allelic distribution was observed at that coverage. Sites with 5-18 reads in both tumor and paired normal but no indication of instability (p>0.05), and those covered by fewer than five reads in either tumor or normal samples were marked as “missing data”.

As a quality control measure, samples were excluded having ≥75% missing data, leaving 9,438 tumor-normal exome pairs and 901 whole genome pairs for subsequent analysis. Similarly, individual loci were excluded for which ≥75% of specimens evidenced missing data.

Gaussian Mixture Model to Classify MSI Status

The overall frequency of microsatellite mutations was quantified for each tumor as the fraction of unstable sites over total callable sites, and given the skewed nature of the data, log₁₀ transformation was performed. For each cancer type, a Gaussian mixture model was then fit to these values using MCLUST v5.4.5 with one or two mixture components with equal variance. If the two-component model could be validly applied to a cancer type, individual tumors were classified as MSS (lower mode), MSI-H (higher mode), or indeterminate (uncertainty value >0.1). If distributions were instead consistent with a single component, all tumors of that cancer type were classified as MSS.

Identifying and Modeling Predictive Abilities of Informative Markers

After excluding “intermediate” MSI classifications, 80% of tumors in each cancer type were randomly assigned into training sets and 20% into validation sets. Using the training sets for each tissue type, microsatellites were identified that were most frequently mutated in MSI-H relative to MSS tumors by Fisher's exact test. The proportions of stable and unstable sites between MSS and MSI-H tumors were compared (excluding missing data), allowing loci to be rank-ordered by p value. For each tissue type, subsets of the top n most informative loci (ranging from 1 to 2,000 markers) were then selected and the percentage of unstable loci for each sample (excluding missing data from both numerator and denominator) was calculated. These values were used to calculate the area under the receiver operating characteristic (AUROC) using pROC v1.15.3. The optimal percentage on the receiver operating characteristic curve was identified by Youden's J statistic. This value was subsequently used as the threshold to assign MSS or MSI-H classification to each sample based on the fraction of mutated markers identified from the simulated panel and to determine sensitivity and specificity for each tissue type.

To account for the possibility of more complex trans-genomic interactions between sites not captured by an additive model of instability, machine learning approaches were explored including random forest and boosted trees. Iterative reduction of marker features was performed using both Fisher exact test p values and Shapley feature importance values in the training dataset. However, these approaches did not meaningfully outperform the simpler, additive model.

Identification of MSI-Associated Microsatellite Mutations Common to Multiple Tissue Types

The top 2,000 loci most strongly associated with MSI-H status for each tissue type were examined for cross-performance across tissue types by hierarchical clustering of normalized p values. Normalization was required to account for differences in the uneven sample sizes, and was accomplished by log 10-transformation of raw p values, followed by scaling on a per-tissue basis from a range of zero (least significant) to one (most significant). A heatmap was generated using superheat v0.1.0, and pairwise and cophenetic distances between tissue types were subsequently calculated and compared using the base-R dist, cophenetic, and cor functions.

Features of Informative Microsatellites

Enrichment of particular locus features (annotated genic context of the repeat, repeat class, and number of repeat subunits in deciles) was examined among individual microsatellite associations with MSI-H status using linear regression. Intergenic annotation, pentanucleotide repeats, and a length of 5-11 repeats, respectively, were arbitrarily selected as reference levels for these analyses. Whole genome data were used for this analysis, as they more comprehensively represented feature annotations across coding and noncoding regions than exome data.

Results: Prevalence of Microsatellite Mutation and MSI-H Tumors Vary Across Cancer Types

To ascertain the relative degree of genomic instability within and across cancer types, the overall frequency of microsatellite mutations was assessed within each of 33 cancer types using paired tumor-normal exome sequencing data. For each cancer type, Gaussian mixture modeling was used to circumscribe subpopulations of tumors having high burdens of microsatellite mutation, corresponding to MSI-H cases (see e.g., FIG. 1A, Table 1; see e.g., Supplemental Table 1 in Appendix A of U.S. Provisional Application No. 63/044,029 filed Jun. 25, 2020, the contents of which are incorporated herein by reference in their entirety). Comparison of MSI classifications established by this approach showed high agreement with determinations made by “gold-standard” MSI-PCR (accuracy 97.8%, 95% CI 95.5%-98.35%) or MOSAIC genome-scale analysis (accuracy 98.8%, 95% CI 98.5%-99.1%), supporting their validity.

TABLE 16 Tumor Exome Sequences and inferred MSI diagnoses Cancer Type (TCGA Fraction of Cases (Count) Code)* MSS Intermediate MSI-H BLCA 0.99 (375) 0.01 (4) 0 (0) BRCA 0.9 (866) 0.04 (43) 0.06 (53) CESC 0.97 (206) 0.005 (1) 0.02 (5) CHOL 0.98 (49) 0 (0) 0.02 (1) COAD 0.79 (309) 0.02 (8) 0.19 (74) DLBC 0.77 (36) 0 (0) 0.23 (11) ESCA 0.98 (145) 0 (0) 0.02 (3) GBM 0.95 (356) 0.01 (4) 0.04 (14) HNSC 0.99 (506) 0.004 (2) 0.01 (4) KICH 1 (64) 0 (0) 0 (0) KIRC 0.97 (321) 0.02 (5) 0.02 (5) KIRP 0.99 (248) 0.004 (1) 0.004 (1) LAML 0.92 (113) 0.07 (8) 0.02 (2) LGG 1 (494) 0 (0) 0.004 (2) LIHC 0.99 (329) 0.003 (1) 0.01 (4) LUAD 0.97 (525) 0.01 (7) 0.02 (10) LUSC 0.96 (436) 0.01 (4) 0.03 (12) MESO 0.98 (59) 0.02 (1) 0 (0) OV 0.87 (339) 0.09 (34) 0.05 (18) PAAD 1 (174) 0 (0) 0 (0) PCPG 1 (184) 0 (0) 0 (0) PRAD 0.99 (455) 0 (0) 0.01 (3) READ 0.94 (133) 0.01 (2) 0.05 (7) SARC 0.99 (186) 0.01 (1) 0.01 (1) SKCM 0.99 (439) 0.005 (2) 0.002 (1) STAD 0.79 (328) 0.005 (2) 0.2 (84) TGCT 1 (156) 0 (0) 0 (0) THCA 1 (454) 0.002 (1) 0 (0) THYM 0.99 (118) 0 (0) 0.01 (1) UCEC 0.57 (255) 0.04 (17) 0.4 (179) UCS 0.96 (55) 0.02 (1) 0.02 (1) UVM 1 (80) 0 (0) 0 (0) In Table 16, “*” indicates the following TCGA codes: BLCA, Bladder Urothelial Carcinoma; BRCA, Breast invasive carcinoma; CESC, Cervical squamous cell carcinoma and endocervical adenocarcinoma; CHOL, Cholangiocarcinoma; COAD, Colon adenocarcinoma; DLBC, Lymphoid Neoplasm Diffuse Large B-cell Lymphoma; ESCA, Esophageal carcinoma; GBM, Glioblastoma multiforme; HNSC, Head and Neck squamous cell carcinoma; KICH, Kidney Chromophobe; KIRC, Kidney renal clear cell carcinoma; KIRP, Kidney renal papillary cell carcinoma; LAML, Acute Myeloid Leukemia; LGG, Brain Lower Grade Glioma; LIHC, Liver hepatocellular carcinoma; LUAD, Lung adenocarcinoma; LUSC, Lung squamous cell carcinoma; MESO, Mesothelioma; OV, Ovarian serous cystadenocarcinoma; PAAD, Pancreatic adenocarcinoma; PCPG, Pheochromocytoma and Paraganglioma; PRAD, Prostate adenocarcinoma; READ, Rectum adenocarcinoma; SARC, Sarcoma; SKCM, Skin Cutaneous Melanoma; STAD, Stomach adenocarcinoma; TGCT, Testicular Germ Cell Tumors; THCA, Thyroid carcinoma; THYM, Thymoma; UCEC, Uterine Corpus Endometrial Carcinoma; UCS, Uterine Carcinosarcoma; UVM, Uveal Melanoma.

Twenty-five of 32 cancer types evidenced one or more hypermutated tumors consistent with an MSI-H phenotype, ranging in incidence from 0.2% to 40%, similar to other reports; see e.g., Hause et al. Nat Med. 2016, 22:1342-50; Cortes-Ciriano et al. Nat Commun. 2017, 8:15180; Bonneville et al. JCO Precision Oncology. 2017, 1-15; the contents of each of which are incorporated herein by reference in their entireties. The total fraction of mutated microsatellites in MSI-H tumors varied considerably across cancer types, with the greatest microsatellite mutation burdens occurring in stomach, colon, and endometrial tumors (see e.g., FIG. 1 ).

Parallel analyses were performed using whole genome data (see e.g., FIG. 5 , Supplemental Table 2 in Appendix A of U.S. Provisional Application No. 63/044,029 filed Jun. 25, 2020, the contents of which are incorporated herein by reference in their entirety), which included intergenic regions but had lower sequencing read depths and were available for fewer cases and cancer types. Although data were sparser, results from whole genome analysis were consistent with those from exome data.

Informative Microsatellite Markers Differ Between Cancer Types

Next, microsatellite mutations most predictive of MSI were identified by cataloging events occurring significantly in MSI-H relative to MSS tumors of each cancer type. This analysis was restricted to cancers for which locus performance could be evaluated in both testing and validation sets, permitting examination of 15 cancer types by exome data alone (see e.g., Supplemental Table 3 in Appendix A of U.S. Provisional Application No. 63/044,029 filed Jun. 25, 2020, the contents of which are incorporated herein by reference in their entirety).

Hierarchical clustering (see e.g., FIG. 2 ) revealed that cancer types displayed markedly different, and largely non-overlapping subsets of informative microsatellites from across the genome. Correlation between measurements of pairwise (see e.g., Table 19) and cophenetic (see e.g., Table 20) distance matrices of locus informativity was 0.82, indicating that clustering accurately represents a large degree of variation in patterns of MSI-associated mutation across cancers. Endometrial and colon tumors were most similar by these metrics, sharing 34.6% of informative sites (4,767 loci), whereas esophageal carcinoma and brain lower grade glioma were most disparate, having only 5% informative microsatellites (79 loci) in common. Similarities in microsatellite mutation patterns were apparent among rectal, stomach, colon and uterine corpus endometrial tumors, as well as between lung adenocarcinoma and squamous cell carcinoma (see e.g., FIG. 2, Supplemental Table 3 in Appendix A of U.S. Provisional Application No. 63/044,029 filed Jun. 25, 2020, the contents of which are incorporated herein by reference in their entirety). However, most cancer types evidenced distinct profiles of microsatellite mutations. Thus, the great majority of loci whose mutation correlates with an MSI-H phenotype are specific to particular cancer types.

Predictive Value of Microsatellites for MSI Diagnosis within and Across Cancer Types

Subsets of one to 2,000 of the most highly informative loci identified per cancer type were used to computationally evaluate their performance for diagnosing MSI within their tumor type of origin, using an independent set of tumor samples for validation (see e.g., FIG. 3 ). Specimens were classified as MSS or MSI-H based on the fraction of mutated microsatellites observed in a given panel, with optimal thresholds for discriminating these classifications determined empirically (see e.g., Table 17). These classifications were compared against determinations made from exome-wide analysis (see e.g., Table 16) to assess their accuracy.

The number of markers needed to achieve MSI diagnosis was initially determined with at least 95% sensitivity and specificity (see e.g., FIG. 3 , Table 17). The number of requisite markers varied considerably across tumor types. For 11 of the 15 cancer types, seven or fewer markers provided the requisite performance characteristics, and in eight cancers MSI could be diagnosed with 100% specificity and sensitivity. Diagnosis of MSI in endometrial tumors required 20 markers, while 65 were needed for classification of kidney renal clear cell cancers. In contrast, MSI determination in breast cancer required 800 markers to achieve comparable performance. MSI diagnosis in ovarian tumors, while favorable for the training set (see e.g., FIG. 3A), did not permit reliable diagnosis in the validation set using any number of markers considered (see e.g., FIG. 3B, Table 17).

The desired balance of sensitivity and specificity can vary by clinical application, and relates to the number of markers examined. Therefore, the predictive capacity of various numbers of markers was additionally determined as measured by the AUROC and the number of makers required to achieve an area under the curve (AUC) of 0.9 or greater (see e.g., Table 17). Although the number of markers required for most cancers by this metric remained similar, decreases for breast (from 800 to 50), kidney renal clear cell (65 to 55), endometrial (20 to 2), and stomach (2 to 1) were observed.

A small number of loci were informative for MSI across multiple cancer types. Therefore, informative microsatellites were examined in endometrial, colon, rectal, and stomach cancers, which collectively showed closely related mutational patterns, in order to determine whether a common marker panel could be used to diagnose MSI in those tumors. After Bonferroni correction, 37 shared microsatellites were independently associated with MSI-H status in each of those four cancer types (see e.g., Table 21). The 37-marker panel demonstrated favorable performance characteristics for the four specific cancer types (0.98 AUC, sensitivity 94.3%, specificity 97.7%), but did not outperform respective tissue-type specific marker panels (see e.g., Table 17) and functioned poorly when applied to other cancers. For example, AUC was 0.45 when the panel was applied to lung squamous cell carcinoma and lung adenocarcinoma, compared with AUC 0.95 for a similarly sized panel specific to those cancer types.

TABLE 17 Performance characteristics of tissue-specific microsatellite panels for MSI diagnosis in validation set; “*” indicates that the cancer did not achieve cutoff for test-characteristic threshold with the maximum number of loci tested. Smallest panel achieving sensitivity and specificity of 95% Min unstable Cancer markers for Type MSI-H (TCGA # of classification Code) markers (%) AUC Sensitivity Specificity COAD 1 50.0% 0.98 100.0% 95.8% ESCA 1 50.0% 1.00 100.0% 100.0% GBM 1 50.0% 1.00 100.0% 100.0% LUAD 1 50.0% 0.99 100.0% 97.1% LUSC 1 50.0% 0.99 100.0% 97.1% READ 2 50.0% 1.00 100.0% 100.0% STAD 2 25.0% 1.00 100.0% 100.0% LGG 5 12.5% 1.00 100.0% 100.0% PRAD 5 16.7% 1.00 100.0% 100.0% CESC 7 45.8% 1.00 100.0% 100.0% UCEC 20 12.9% 0.98 97.0% 97.9% KIRC 65 7.5% 0.99 100.0% 98.5% BRCA 800 3.6% 1.00 100.0% 99.5% OV* 2000 2.0% 0.63 100.0% 47.8% Smallest panel achieving AUROC of 0.9 Min unstable markers for MSI-H # of classification markers (%) AUC Sensitivity Specificity COAD 1 50.0% 0.98 100.0% 95.8% ESCA 1 50.0% 1.00 100.0% 100.0% GBM 1 50.0% 1.00 100.0% 100.0% LUAD 1 50.0% 0.99 100.0% 97.1% LUSC 1 50.0% 0.99 100.0% 97.1% READ 2 50.0% 1.00 100.0% 100.0% STAD 1 50.0% 0.92 84.2% 100.0% LGG 5 12.5% 1.00 100.0% 100.0% PRAD 5 16.7% 1.00 100.0% 100.0% CESC 7 45.8% 1.00 100.0% 100.0% DLBC 7 25.0% 1.00 100.0% 100.0% UCEC 2 25.0% 0.95 90.3% 97.2% KIRC 55 4.6% 0.93 100.0% 86.6% BRCA 50 4.3% 0.92 100.0% 81.1% OV* 2000 2.0% 0.63 100.0% 47.8%

Properties of Informative Microsatellites

The sequence composition and genic feature annotations that were enriched in microsatellites having globally high informativity were examined for MSI-H tumors (see e.g., FIG. 4 , Table 22). Whole genome data were examined in order to allow exploration of coding and noncoding regions; this approach showed agreement with analyses of exome sequencing where direct comparisons were possible (data not shown). Of the different types of repeat sequence classes examined (see e.g., FIG. 4A), mononucleotide microsatellite mutations correlated most highly with MSI-H, followed by complex repeats (which themselves may be composed of multiple mononucleotide repeats). MSI-informative markers were most significantly enriched in splice sites (see e.g., FIG. 4B), and conversely, intergenic regions and noncoding intronic annotations contained the fewest informative microsatellites elements. Notably, a non-linear correlation was found between the length of mononucleotide markers and their informativity (see e.g., FIG. 4C and FIG. 4D). Tracts comprised of 12 to 13 repeats proved most informative, with longer or shorter loci showing a decrease in informativity proportional to their distance from this maximum.

CONCLUSIONS

Herein, genomic analyses were used to prioritize microsatellite markers that are most informative for diagnosing MSI by molecular methods. Whereas other work has cataloged loci that are frequently mutated in MSI-H tumors from the three or four cancer types where the phenotype occurs most often (see e.g., Hause et al., 2016, supra; Cortes-Ciriano et al., 2017, supra), herein microsatellite mutation occurrence was more broadly examined across cancer types and the performance of variously sized marker subsets was also evaluated for classifying MSI-H tumors in clinical practice.

Cancer types exhibit distinct patterns of microsatellite mutation overall, and herein it was found that microsatellites that are informative for diagnosing MSI also vary across cancer types (see e.g., FIG. 2 ). These results strongly argue that MSI diagnostic panels developed for particular tumor types should not be considered generally applicable across all cancers. Although a small subset of markers was cross-informative across a limited group of cancer types that shared similar mutational profiles (see e.g., Table 17), microsatellites tailored to a specific cancer type provided maximal diagnostic accuracy.

Accordingly, in determining markers with the highest diagnostic utility (see e.g., FIG. 4 ), it was observed that microsatellite mutations within functional elements including splice sites and exons were significantly enriched, supporting the notion that biological pressures are involved in selecting microsatellite mutations associated with MSI. It was also observed that mononucleotide microsatellites, loci occurring in splicing regions, and microsatellites comprised of 12 to 13 repeat subunits provided the greatest diagnostic benefit, with microsatellites of 18 or greater repeats being significantly associated with stability. This latter finding indicates that, unlike in in vitro systems, MSI phenotypes in vivo preferentially involve tracts of specific lengths.

The performance was evaluated of variously sized subsets of the most informative loci per cancer type in data sets withheld from those used to identify informative loci (see e.g., FIG. 3 , Table 17). Due to the degree of missing microsatellite calls inherent to the dataset, existing performance estimates are likely to be conservative. Even so, eight of the 15 cancer types achieved 100% sensitivity and specificity using seven or fewer loci, and in two of those cancer types only a single marker was required. These modest testing requirements are compatible with MSI diagnosis by highly focused methods including conventional MSI-PCR or targeted NGS. Endometrial and kidney renal clear cell tumors required slightly more markers (20 and 65, respectively). In two extreme cases, breast cancer required 800 markers whereas reliable MSI diagnosis could not be achieved in ovarian cancer using pre-defined subsets of microsatellite markers. These findings are consistent with microsatellites following less stereotyped patterns of mutation for breast and ovarian cancers, possibly owing to instability events having more neutral fitness effects for breast and ovarian tumors and subsequently resulting in fewer recurrently mutated loci. In these cancer types, and possibly others, a measurement of overall genome-wide microsatellite mutation burden can be required to reliably establish MSI diagnosis (see e.g., FIG. 1 ).

Although MSI status is currently an approved diagnostic marker to indicate eligibility for PDL-1 and PD-1 inhibitor treatments, alternative methods for testing tumor susceptibility to those immunotherapies are now available. The most widely used of these alternative approaches is tumor mutation burden (TMB), a biomarker based on estimating the total substitution and indel lesions present in a cancer genome. Nevertheless, TMB determination requires sequencing large gene panels and is of contested clinical utility. Because immunotherapy response is particularly associated with insertion-deletion mutational load, MSI is considered a more reliable positive predictor of treatment outcomes even though it is unable to identify all cancers for which a favorable response can be achieved. Although MSI and TMB determinations frequently overlap, they provide distinct information. Given these considerations, MSI and TMB can be considered complementary, and dedicated testing for MSI can continue to provide utility as an inexpensive, primary screening method for immunotherapy response.

The tissue-specific diagnostic performance of loci identified herein could not be directly compared to microsatellite loci included in clinical MSI assays due to both the unknown sensitivity of NGS relative to MSI-PCR for detecting microsatellite mutations and inadequate read depths for those markers in both exome and whole genome data. It is noteworthy that the most informative markers identified by these analyses do not overlap with those utilized in standard clinical assays for MSI.

Nonstandard abbreviations include the following: MSI, microsatellite instability; MMR, mismatch repair; MSI-H, microsatellite instability high; MSS, microsatellite stable; NGS, Next-Generation DNA sequencing; TMB, tumor mutation burden; AUC, area under the curve; AUROC, area under the receiver operating characteristic. Human gene abbreviations include at least the following: PD-1, programmed cell death 1; PDL-1, programmed cell death 1 ligand 1. All gene abbreviations herein (e.g., in Tables 1-15) are used as known in art.

References include the following, the contents of each of which are incorporated herein by reference in their entireties:

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TABLE 19 Pairwise Euclidean dissimilarity matrix of tissue-specific informative microsatellite loci based on tissue-scaled p-values. UCEC STAD READ PRAD OV LUSC LUAD LGG KIRC GBM ESCA DLBC COAD CESC BRCA UCEC 0 10.7 13.8 18.2 17.2 16.6 16.6 20.8 17.4 16.8 17.1 18.9 9.3 15 12.4 STAD 10.7 0 16.1 19.3 19.5 18.7 18.4 22.8 19.3 18.7 19.6 21.8 12.5 18 15.4 READ 13.8 16.1 0 19.9 18.8 18.2 18.6 22.1 19.7 18.9 20.4 19.8 13.1 17.9 15.7 PRAD 18.2 19.3 19.9 0 16 13.7 14.6 18.2 18.7 15 21.2 15.9 19.2 16.2 15.4 OV 17.2 19.5 18.8 16 0 11.6 12.8 16.7 17 13.2 20.3 13 18.3 14.4 13.4 LUSC 16.6 18.7 18.2 13.7 11.6 0 9.9 14.4 15.5 10.4 19.4 10.6 17.8 12.4 11.8 LUAD 16.6 18.4 18.6 14.6 12.8 9.9 0 15.6 16.2 11.2 19.7 12.2 17.9 13.3 12.5 LGG 20.8 22.8 22.1 18.2 16.7 14.4 15.6 0 19.7 15.6 23 15.8 22 17.2 16.8 KIRC 17.4 19.3 19.7 18.7 17 15.5 16.2 19.7 0 16.4 21.9 17 18.8 17.2 15.8 GBM 16.8 18.7 18.9 15 13.2 10.4 11.2 15.6 16.4 0 20 12.4 18.3 13.8 12.6 ESCA 17.1 19.6 20.4 21.2 20.3 19.4 19.7 23 21.9 20 0 20.9 18.3 18.3 18.2 DLBC 18.9 21.8 19.8 15.9 13 10.6 12.2 15.8 17 12.4 20.9 0 19.8 14.3 13.8 COAD 9.3 12.5 13.1 19.2 18.3 17.8 17.9 22 18.8 18.3 18.3 19.8 0 16.5 14 CESC 15 18 17.9 16.2 14.4 12.4 13.3 17.2 17.2 13.8 18.3 14.3 16.5 0 13.1 BRCA 12.4 15.4 15.7 15.4 13.4 11.8 12.5 16.8 15.8 12.6 18.2 13.8 14 13.1 0

TABLE 20 Pairwise Cophenetic dissimilarity matrix of tissue-specific informative microsatellite loci based on tissue-scaled p-values. UCEC STAD READ PRAD OV LUSC LUAD LGG KIRC GBM ESCA DLBC COAD CESC BRCA UCEC 0 12.5 16.1 23 23 23 23 23 19.7 23 21.9 23 9.3 23 23 STAD 12.5 0 16.1 23 23 23 23 23 19.7 23 21.9 23 12.5 23 23 READ 16.1 16.1 0 23 23 23 23 23 19.7 23 21.9 23 16.1 23 23 PRAD 23 23 23 0 16.2 16.2 16.2 18.2 23 16.2 23 16.2 23 16.2 16.2 OV 23 23 23 16.2 0 13.2 13.2 18.2 23 13.2 23 13.2 23 14.4 14.4 LUSC 23 23 23 16.2 13.2 0 9.9 18.2 23 11.2 23 12.4 23 14.4 14.4 LUAD 23 23 23 16.2 13.2 9.9 0 18.2 23 11.2 23 12.4 23 14.4 14.4 LGG 23 23 23 18.2 18.2 18.2 18.2 0 23 18.2 23 18.2 23 18.2 18.2 KIRC 19.7 19.7 19.7 23 23 23 23 23 0 23 21.9 23 19.7 23 23 GBM 23 23 23 16.2 13.2 11.2 11.2 18.2 23 0 23 12.4 23 14.4 14.4 ESCA 21.9 21.9 21.9 23 23 23 23 23 21.9 23 0 23 21.9 23 23 DLBC 23 23 23 16.2 13.2 12.4 12.4 18.2 23 12.4 23 0 23 14.4 14.4 COAD 9.3 12.5 16.1 23 23 23 23 23 19.7 23 21.9 23 0 23 23 CESC 23 23 23 16.2 14.4 14.4 14.4 18.2 23 14.4 23 14.4 23 0 13.1 BRCA 23 23 23 16.2 14.4 14.4 14.4 18.2 23 14.4 23 14.4 23 13.1 0

TABLE 21 Coordinates of cross-informative microsatellites for diagnosing MSI in endometrial, colon, rectal, and stomach cancers. Start End Start End Start End Chromosome Position Position Chromosome Position Position Chromosome Position Position 1 149900985 149901002 16 3808052 3808066 6 102130410 102130422 1 222904869 222904881 16 9010826 9010844 6 122733490 122733508 10 112360315 112360333 17 29508819 29508836 6 36452603 36452620 10 35314130 35314161 19 6026288 6026302 6 46636556 46636581 10 64022582 64022593 2 141294271 141294299 6 49415351 49415368 11 118885668 118885701 2 203676382 203676403 7 97939975 97939988 12 110834030 110834049 2 32095023 32095056 8 100160282 100160300 12 125587478 125587491 2 8998775 8998788 8 33356825 33356839 12 85285920 85285938 3 41877473 41877487 9 52625 52641 12 89853387 89853405 4 146031236 146031253 9 75420448 75420463 13 79216356 79216381 5 172578549 172578567 X 106092450 106092473 15 55841195 55841209 5 36123065 36123135 X 19380975 19380993 16 10567751 10567778

TABLE 22 Covariates associated with instability of MSI-informative microsatellites. “*” indicates that the Positive coefficients values are associated with microsatellite instability; negative values are associated with microsatellite stability “**” indicates that the category was used as reference for statistical comparisons. Feature Category Feature Coefficient* 97.5% confidence interval p value Coding context Intergenic Not applicable** Upstream 0.26330362 0.201082791 to 0.32552445  1.1E−16 Downstream 0.24775092 0.19523743 to 0.3002644 2.32E−20 Exonic 0.63116873 0.312458773 to 0.94987869 0.000104 Intronic 0.22357372 0.214076632 to 0.23307081 0 ncRNA exonic 0.24869416 0.139176607 to 0.35821171 8.56E−06 ncRNA intronic 0.06674437 0.045628207 to 0.08786053 5.83E−10 ncRNA splicing 0.80560147 0.355024088 to 1.25617886 0.000458 Splicing 1.095599 0.889927325 to 1.30127068 1.63E−25 Upstream and Downstream 0.20875388 −0.103550755 to 0.52105852  0.190162 3′ UTR 0.54949742 0.502719112 to 0.59627574  3.1E−117 5′ UTR 0.64615781 0.442216539 to 0.85009909 5.31E−10 5′ UTR5 and 3′ UTR 0.0103701 −3.508426006 to 3.52916621  0.995391 Repeat class Compound repeat 1.46871369 1.301270946 to 1.63615644 3.18E−66 Complex repeat 0.92271293 0.751505079 to 1.09392078 4.44E−26 Mononucleotide repeat 1.44146313 1.272848876 to 1.61007737 5.33E−63 Dinucleotide repeat 0.15687561 −0.012360733 to 0.32611194  0.069246 Trinucleotide repeat −0.118346  −0.4131167 to 0.17642471 0.431342 Tetranucleotide Repeat 0.24265869 0.054478379 to 0.43083901 0.011492 Pentanucleotide Repeat Not applicable** Number of repeats  5-11 Not applicable** 11-12 0.80031813 0.779980199 to 0.82065606 0 12-13 1.77745115 1.757111464 to 1.79779084 0 13-14 1.59183987 1.571499926 to 1.61217982 0 14-16 1.50008182 1.479731404 to 1.52043224 0 16-18 0.31325393  0.2920993 to 0.33440855  4.6E−185 18-21 −0.1869956 −0.211463299 to −0.162528  1.03E−50 21-25 −0.2282874 −0.255785148 to −0.2007896  1.61E−59 25-32 −0.5444188 −0.572807037 to −0.5160306  0 >32 −1.2434585 −1.272243027 to −1.2146739  0

Example 2: Supplemental Information

For full versions of the Supplemental Tables 1-3 described in EXAMPLE 1 above, please see APPENDIX A of U.S. Provisional Application No. 63/044,029 filed Jun. 25, 2020, the contents of which are incorporated herein by reference in their entirety.

Please see APPENDIX B of U.S. Provisional Application No. 63/044,029 filed Jun. 25, 2020, the contents of which are incorporated herein by reference in their entirety, for a table of microsatellite sequences most significantly associated with MSI-H classification for each cancer type. The location of each microsatellite is listed according to hg19 coordinates; and the p value for significance is indicated for each specified cancer type. Blank cells indicate non-significant values. See also Tables 1-15 herein. 

1. A method of predicting whether a subject's cancer will respond to checkpoint inhibitor immunotherapy, the method comprising: (a) receiving microsatellite instability data for a defined set of microsatellite repeat marker sequences in cells of the subject's cancer; and (b) processing the microsatellite instability data to output a categorical measure of microsatellite instability high (MSI-H) or microsatellite stable (MSS); wherein when the subject's cancer is determined to exhibit MSI-H, it is predicted that the cancer will respond to checkpoint inhibitor immunotherapy, and when the subject's cancer is determined to exhibit MSS, it is predicted that the cancer is less likely to respond to checkpoint inhibitor immunotherapy.
 2. (canceled)
 3. The method of claim 1, wherein processing the microsatellite instability data to output a categorical measure of microsatellite instability high (MSI-H) or microsatellite stable (MSS) comprises applying a quantitative model relating the predictive capability of the markers in the set or a subset thereof to known MSI status.
 4. The method of claim 3, wherein the quantitative model: is selected from a continuous measure, regression or weighted scoring of markers, a combinatorial or decision-tree model, and a machine learning model; comprises a random-forest model or a deep neural network machine learning model; or evaluates or incorporates consideration of one or more test characteristics selected from the group consisting of sensitivity, accuracy, correlation, probability, specificity, false-positive rate, false negative rate, positive predictive value, negative predictive value and area under the receiver-operator characteristic (AUROC).
 5. The method of claim 4, wherein the continuous measure comprises the proportion of unmutated or stable loci to mutated or unstable loci detected in the set. 6-7. (canceled)
 8. The method of claim 4, wherein thresholds for the one or more test characteristics indicative of MSI-H or MSS are defined within parameters of the known test characteristics for a given clinical application.
 9. The method of claim 1, wherein: when the cancer is colon adenocarcinoma (COAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 1; when the cancer is esophageal carcinoma (ESCA), the set of microsatellite repeat marker sequences comprises a plurality up to 503 of the microsatellites set out in Table 2; when the cancer is glioblastoma multiforme (GBM), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 3; when the cancer is lung adenocarcinoma (LUAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 4; when the cancer is lung squamous cell carcinoma (LUSC), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 5; when the cancer is rectum adenocarcinoma (READ), the set of microsatellite repeat marker sequences comprises a plurality up to 501 of the microsatellites set out in Table 6; when the cancer is stomach adenocarcinoma (STAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 7; when the cancer is brain lower grade glioma (LGG), the set of microsatellite repeat marker sequences comprises a plurality up to 266 of the microsatellites set out in Table 8; when the cancer is prostate adenocarcinoma (PRAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 9; when the cancer is cervical squamous cell carcinoma (CESC), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 10; when the cancer is lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), the set of microsatellite repeat marker sequences comprises a plurality up to 212 of the microsatellites set out in Table 11; when the cancer is uterine corpus endometrial carcinoma (UCEC), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 12; when the cancer is kidney renal clear cell carcinoma (KIRC), the set of microsatellite repeat marker sequences comprises a plurality up to 508 of the microsatellites set out in Table 13; when the cancer is breast invasive carcinoma (BRCA), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 14A; and when the cancer is uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or stomach adenocarcinoma (STAD), the set of microsatellite repeat marker sequences comprises a plurality up to 37 of the microsatellites set out in Table
 21. 10-11. (canceled)
 12. The method of claim 1, wherein the set of microsatellite repeat marker sequences comprises a plurality up to the first 100 of the sequences set out in the respective Table for the subject's cancer type. 13-16. (canceled)
 17. The method of claim 1, wherein the processing of MSI-H or MSS is determined by a threshold value for the set of microsatellite marker sequences.
 18. The method of claim 17, wherein the threshold for the set of microsatellite marker sequences is determined using the percentage of mutated microsatellite markers in the set to calculate the area under the receiver operating characteristic (AUROC).
 19. The method of claim 18, wherein the smallest number of markers in the set necessary to reach a selected AUROC value is the threshold.
 20. The method of claim 19, wherein the selected AUROC value is a value between 0.6 and 0.99, inclusive.
 21. The method of claim 19, wherein the selected AUROC value is 0.9 or more. 22-25. (canceled)
 26. The method of claim 1, wherein microsatellite mutations correspond to those identified in reference human genome GRCh37/hg19 translated to a different build of the human reference genome. 27-42. (canceled)
 43. A method of treating cancer in a subject in need thereof, the method comprising determining microsatellite instability status for cells of a subject's cancer by a method of claim 1, and, when the microsatellite instability status is determined to be MSI-H, administering a checkpoint inhibitor, or, when the microsatellite instability status is determined to be MSS, administering a non-checkpoint inhibitor cancer therapeutic.
 44. The method of claim 43, wherein the checkpoint inhibitor is an inhibitor of a checkpoint molecule selected from the group consisting of: PD-1 or PD-L1, CTLA4, Adenosine A2A receptor (A2AR), CD276, CD39, CD73, B7 family immune checkpoint molecules, V-set domain-containing T-cell activation inhibitor 1 (B7H4), B and T Lymphocyte Attenuator (BTLA), Indoleamine 2,3-dioxygenase (IDO), Killer-cell Immunoglobulin-like Receptor (KIR), Lymphocyte Activation Gene-3 (LAG3), nicotinamide adenine dinucleotide phosphate NADPH oxidase isoform 2 (NOX2), T-cell Immunoglobulin domain and Mucin domain 3 (TIM-3), T cell immunoreceptor with Ig and ITIM domains (TIGIT), V-domain Ig suppressor of T cell activation (VISTA), and Sialic acid-binding immunoglobulin-type lectin 7 (SIGLEC7).
 45. The method of claim 43, wherein the checkpoint inhibitor is selected from the group consisting of pembrolizumab (Keytruda®), nivolumab (Opdivo®), cemiplimab (Libtayo®), spartalizumab, camrelizumab, sintilimab, tislelizumab, toripalimab, dostarlimab, INVMGA00012, AMP-224, AMP-514, atezolizumab (Tecentriq®), avelumab (Bavencio®), survalumab (Imfinzi®), KN035, CK-301, AUNP12, CA-170, BMS-986189, and ipilimumab (Yervoy®). 46-47. (canceled)
 48. The method of claim 43, wherein the non-checkpoint inhibitor cancer therapy comprises one or more of angiostatin K1-3, DL-a-Difluoromethyl-ornithine, endostatin, fumagillin, genistein, minocycline, staurosporine, and (±)-thalidomide; a DNA intercalator/cross-linker, such as Bleomycin, Carboplatin, Carmustine, Chlorambucil, Cyclophosphamide, cis-Diammineplatinum(II) dichloride (Cisplatin), Melphalan, Mitoxantrone, and Oxaliplatin; a DNA synthesis inhibitor, such as (±)-Amethopterin (Methotrexate), 3-Amino-1,2,4-benzotriazine 1,4-dioxide, Aminopterin, Cytosine β-D-arabinofuranoside, 5-Fluoro-5′-deoxyuridine, 5-Fluorouracil, Ganciclovir, Hydroxyurea, and Mitomycin C; a DNA-RNA transcription regulator, such as Actinomycin D, Daunorubicin, Doxorubicin, Homoharringtonine, and Idarubicin; an enzyme inhibitor, such as S(+)-Camptothecin, Curcumin, (−)-Deguelin, 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside, Etoposide, Formestane, Fostriecin, Hispidin, 2-Imino-1-imidazoli-dineacetic acid (Cyclocreatine), Mevinolin, Trichostatin A, Tyrphostin AG 34, and Tyrphostin AG 879; a gene regulator, such as 5-Aza-2′-deoxycytidine, 5-Azacytidine, Cholecalciferol (Vitamin D3), 4-Hydroxytamoxifen, Melatonin, Mifepristone, Raloxifene, all trans-Retinal (Vitamin A aldehyde), Retinoic acid, all trans (Vitamin A acid), 9-cis-Retinoic Acid, 13-cis-Retinoic acid, Retinol (Vitamin A), Tamoxifen, and Troglitazone; a microtubule inhibitor, such as Colchicine, Dolastatin 15, Nocodazole, Paclitaxel, Podophyllotoxin, Rhizoxin, Vinblastine, Vincristine, Vindesine, and Vinorelbine (Navelbine); a neoantigen; and an unclassified antitumor agent, such as 17-(Allylamino)-17-demethoxygeldanamycin, 4-Amino-1, 8-naphthalimide, Apigenin, Brefeldin A, Cimetidine, Dichloromethylene-diphosphonic acid, Leuprolide (Leuprorelin), Luteinizing Hormone-Releasing Hormone, Pifithrin-α, Rapamycin, Sex hormone-binding globulin, Thapsigargin, and Urinary trypsin inhibitor fragment (Bikunin), Vemurafenib (Zelboraf®) imatinib mesylate (Gleevec®), erlotinib (Tarceva®), gefitinib (Iressa®), Vismodegib (Erivedge™), 90Y-ibritumomab tiuxetan, regorafenib (Stivarga®), sunitinib (Sutent®), Denosumab (Xgeva®), sorafenib (Nexavar®), pazopanib (Votrient®), axitinib (Inlyta®), dasatinib (Sprycel®), nilotinib (Tasigna®), bosutinib (Bosulif®), ofatumumab (Arzerra®), obinutuzumab (Gazyva™), ibrutinib (Imbruvica™), idelalisib (Zydelig®), crizotinib (Xalkori®), erlotinib (Tarceva®), afatinib dimaleate (Gilotrif®), ceritinib (LDK378/Zykadia), ibritumomab tiuxetan (Zevalin®), brentuximab vedotin (Adcetris®), bortezomib (Velcade®), siltuximab (Sylvant™), trametinib (Mekinist®), dabrafenib (Tafinlar®), a targeted therapy such as toremifene (Fareston®), fulvestrant (Faslodex®), anastrozole (Arimidex®), exemestane (Aromasin®), letrozole (Femara®), ziv-aflibercept (Zaltrap®), Alitretinoin (Panretin®), temsirolimus (Torisel®), Tretinoin (Vesanoid®), denileukin diftitox (Ontak®), vorinostat (Zolinza®), romidepsin (Istodax®), bexarotene (Targretin®), pralatrexate (Folotyn®), lenaliomide (Revlimid®), belinostat (Beleodaq™), lenaliomide (Revlimid®), pomalidomide (Pomalyst®), Cabazitaxel (Jevtana®), enzalutamide (Xtandi®), abiraterone acetate (Zytiga®), radium 223 chloride (Xofigo®), or everolimus (Afinitor®), an epigenetic targeted drug such as HDAC inhibitors, azacitidine (Vidaza®), decitabine (Dacogen®), vorinostat (Zolinza®), romidepsin (Istodax®), ruxolitinib (Jakafi®), kinase inhibitors, DNA methyltransferase inhibitors, histone demethylase inhibitors, or histone methylation inhibitors, and any derivative thereof. 49-54. (canceled)
 55. The method of claim 1, wherein when mutations are present in at least a threshold number of markers in the set, the set provides at least 95% sensitivity and at least 95% specificity for predicting high microsatellite instability (MSI-H) for the subject's tumor, wherein: when the cancer is colon adenocarcinoma (COAD), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 1 and the threshold number is 50%; when the cancer is esophageal carcinoma (ESCA), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 2 and the threshold number is 50%; when the cancer is glioblastoma multiforme (GBM), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 3 and the threshold number is 50%; when the cancer is lung adenocarcinoma (LUAD), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 4 and the threshold number is 50%; when the cancer is lung squamous cell carcinoma (LUSC), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 5 and the threshold number is 50%; when the cancer is rectum adenocarcinoma (READ), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 6 and the threshold number is 50%; when the cancer is stomach adenocarcinoma (STAD), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 7 and the threshold number is 25%; when the cancer is brain lower grade glioma (LGG), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 8 and the threshold number is 12.5%; when the cancer is prostate adenocarcinoma (PRAD), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 9 and the threshold number is 16.7%; when the cancer is cervical squamous cell carcinoma (CESC), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 10 and the threshold number is 45.8%; when the cancer is lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 11 and the threshold number is 25%; when the cancer is uterine corpus endometrial carcinoma (UCEC), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 12 and the threshold number is 12.9%; when the cancer is kidney renal clear cell carcinoma (KIRC), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 13 and the threshold number is 7.5%; when the cancer is breast invasive carcinoma (BRCA), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 14A and the threshold number is 3.6%; and when the cancer is uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or stomach adenocarcinoma (STAD), the microsatellite repeat marker sequences comprise a plurality of microsatellite repeat markers in Table 21 and the threshold number is at least 12.9%; and wherein when the subject's cancer exhibits greater than or equal to the threshold number of mutations for that tumor type in the set, the subject's cancer is determined to be MSI-H, and is predicted to be sensitive to checkpoint inhibitor immunotherapy. 56-100. (canceled)
 101. A diagnostic kit for determining microsatellite instability in a cancer, the kit comprising reagents that permit the detection of microsatellite mutation in a set of microsatellite repeat marker sequences in the cancer, wherein: when the cancer is colon adenocarcinoma (COAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 1; when the cancer is esophageal carcinoma (ESCA), the set of microsatellite repeat marker sequences comprises a plurality up to 503 of the microsatellites set out in Table 2; when the cancer is glioblastoma multiforme (GBM), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 3; when the cancer is lung adenocarcinoma (LUAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 4; when the cancer is lung squamous cell carcinoma (LUSC), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 5; when the cancer is rectum adenocarcinoma (READ), the set of microsatellite repeat marker sequences comprises a plurality up to 501 of the microsatellites set out in Table 6; when the cancer is stomach adenocarcinoma (STAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 7; when the cancer is brain lower grade glioma (LGG), the set of microsatellite repeat marker sequences comprises a plurality up to 266 of the microsatellites set out in Table 8; when the cancer is prostate adenocarcinoma (PRAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 9; when the cancer is cervical squamous cell carcinoma (CESC), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 10; when the cancer is lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), the set of microsatellite repeat marker sequences comprises a plurality up to 212 of the microsatellites set out in Table 11; when the cancer is uterine corpus endometrial carcinoma (UCEC), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 12; when the cancer is kidney renal clear cell carcinoma (KIRC), the set of microsatellite repeat marker sequences comprises a plurality up to 508 of the microsatellites set out in Table 13; when the cancer is breast invasive carcinoma (BRCA), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 14A; and when the cancer is uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or stomach adenocarcinoma (STAD), the set of microsatellite repeat marker sequences comprises a plurality up to 37 of the microsatellites set out in Table
 21. 102-108. (canceled)
 109. An array for detecting microsatellite instability in a cancer, the array comprising nucleic acids that permit the detection of microsatellite mutation in a set of microsatellite repeat marker sequences in the cancer, wherein the nucleic acids are linked to a solid support, wherein the nucleic acids are complementary to at least a portion of the microsatellite sequences, and wherein: when the cancer is colon adenocarcinoma (COAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 1; when the cancer is esophageal carcinoma (ESCA), the set of microsatellite repeat marker sequences comprises a plurality up to 503 of the microsatellites set out in Table 2; when the cancer is glioblastoma multiforme (GBM), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 3; when the cancer is lung adenocarcinoma (LUAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 4; when the cancer is lung squamous cell carcinoma (LUSC), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 5; when the cancer is rectum adenocarcinoma (READ), the set of microsatellite repeat marker sequences comprises a plurality up to 501 of the microsatellites set out in Table 6; when the cancer is stomach adenocarcinoma (STAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 7; when the cancer is brain lower grade glioma (LGG), the set of microsatellite repeat marker sequences comprises a plurality up to 266 of the microsatellites set out in Table 8; when the cancer is prostate adenocarcinoma (PRAD), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 9; when the cancer is cervical squamous cell carcinoma (CESC), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 10; when the cancer is lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), the set of microsatellite repeat marker sequences comprises a plurality up to 212 of the microsatellites set out in Table 11; when the cancer is uterine corpus endometrial carcinoma (UCEC), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 12; when the cancer is kidney renal clear cell carcinoma (KIRC), the set of microsatellite repeat marker sequences comprises a plurality up to 508 of the microsatellites set out in Table 13; when the cancer is breast invasive carcinoma (BRCA), the set of microsatellite repeat marker sequences comprises a plurality up to 500 of the microsatellites set out in Table 14A; and when the cancer is uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), or stomach adenocarcinoma (STAD), the set of microsatellite repeat marker sequences comprises a plurality up to 37 of the microsatellites set out in Table
 21. 110-117. (canceled) 